Method of predicting risk of lung cancer recurrence, and a composition, kit and microarray for the same

ABSTRACT

Provided is a method of predicting risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, the method including: obtaining a biological sample from a lung cancer patient; measuring an expression level of at least one marker gene from the biological sample, the marker gene being selected from the group consisting of marker genes of Table 1, 2 or 3, to obtain data for the expression level of the marker gene; and determining whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group.

CROSS-REFERENCE TO RELATED PATENT APPLICATION

This application is a division application of U.S. patent application Ser. No. 11/971585, filed Jan. 9, 2008, which claims priority to Korean Patent Application No. 10-2007-0002643, filed on Jan. 9, 2007, the disclosure of each of which is incorporated herein in its entirety by reference.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to a method of predicting risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, a method of preparing a report on the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, a report prepared by the same, and a composition, kit and microarray for diagnosing the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment.

2. Description of the Related Art

Lung cancer is the leading cause of death due to cancer in the world. Lung cancer is categorized into two types, small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), and about 80% of lung cancer cases are categorized as NSCLC. NSCLC is categorized into three sub-types: 40% of adenocarcinoma, 40% of squamous cell carcinoma and 20% of large cell carcinoma. Currently, a TMN staging system is widely accepted in the management of lung cancer.

In the TMN staging system, the primary tumor is subdivided into four T categories (T1-T4) depending upon the tumor size, site and local involvement. Lymph node spread is subcategorized into bronchio/pulmonary within the lung (N1), mediastinal spread on the same side of the lung as the primary tumor (N2) and mediastinal spread on the side of the lung opposite to the side having the primary tumor or supraclavicular involvement (N3). Distal or metastatic spread is either absent or present (M0 or M1). In general, lung cancer that does not metastasize is treated by being removed through a surgical operation. However, recurrence rate after a lung cancer removal operation is as high as 20 to 50% (Cancer: Principles & Practice of Oncology, 56th. ed. In: Devita D V, Hellman S, Rosenberg S A, eds. Philadelphia, Pa.: Lippincott Williams & Wilkins, 2001).

Conventionally, a method of diagnosing lung cancer using a marker gene specific to lung cancer is known. For example, U.S. Patent Publication No.2006025057 discloses a method of diagnosing lung cancer using a marker specific to lung cancer. Further, U.S. Patent Publication No.20050272061 discloses a method of diagnosing cancer in an individual, comprising measuring an L gene that is specifically and distinctively expressed in lung cancer tissues and cells, and its products.

However, there is still a need for developing a method of effectively predicting the risk of lung cancer recurrence in a lung cancer patient or a patient who has had lung cancer treatment to the extent that the method is applied to clinical practices.

SUMMARY OF THE INVENTION

The present invention provides a method of predicting risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment.

The present invention also provides a method of preparing a report on the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment and a report prepared by the same.

The present invention also provides a composition, kit and microarray for diagnosing the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment.

According to an aspect of the present invention, there is provided a method of predicting risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, the method comprising:

obtaining a biological sample from a lung cancer patient;

measuring an expression level of at least one marker gene from the biological sample, the marker gene being selected from the group consisting of marker genes of Table 1, 2 or 3 to obtain data for the expression level of the marker gene; and

determining whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group.

The method of predicting risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment includes obtaining a biological sample from a lung cancer patient.

The obtaining a biological sample may include any operation that obtains a sample including an arbitrary cell from a lung cancer patient. For example, the biological sample may be blood, plasma, serum, urine, tissue, cell, organ, bone marrow, saliva, expectoration, cerebrospinal fluid and the like, but is not limited thereto. The biological sample may be preferably lung cancer tissue. The biological sample may be lung cancer tissue removed during a lung cancer removal operation, but is not necessarily obtained by the lung cancer removal operation. The obtainment of the lung cancer tissue may be physically conducted or optically conducted through a laser or the like.

The method of predicting a risk of lung cancer recurrence in a lung cancer patient or a patient after a lung cancer treatment includes measuring an expression level of at least one marker gene selected from the group consisting of marker genes of Table 1, 2 or 3 in the sample to obtain data for the expression level of the marker gene.

The measuring an expression level of the marker gene may be performed by measuring an expression level of at least one marker gene selected from the group consisting of marker genes of Table 1. Preferably, in this operation, expression levels of at least 2, 4, 6, 8, 10, 15, 20, 30, 70, 100, 150 or a total of 166 marker genes selected from the group consisting of marker genes of Table 1 may be measured. In this case, the lung cancer may be adenocarcinoma or squamous cell carcinoma.

When the lung cancer is adenocarcinoma, the measuring an expression level of the marker gene may be performed by measuring an expression level of at least one marker gene selected from the group consisting of marker genes of Table 2. Preferably, in this operation, expression levels of at least 2, 4, 6, 8, 10, 15, 20, 30, 70, 100, 150, 200, 250 or a total of 300 marker genes selected from the group consisting of marker genes of Table 2 may be measured.

When the lung cancer is squamous cell carcinoma, the measuring an expression level of the marker gene may be performed by measuring an expression level of at least one marker gene selected from the group consisting of marker genes of Table 3. Preferably, in this operation, an expression level of at least 2, 4, 6, 8, 10, 15, 20, 30, 70, 100, 150, or a total of 166 marker genes selected from the group consisting of marker genes of Table 3 may be measured.

The measuring an expression level of the marker gene includes measuring an arbitrary expression product expressed from the maker gene. For example, this operation may be measuring a level of mRNA or protein derived from the marker gene.

The “measurement of a level of mRNA” may be analyzed using a conventional method including RT-PCR, competitive RT-PCR, real-time RT-PCR, RNase protection assay, northern blotting, DNA microarray and the like. Preferably, the measurement of a level of mRNA may be carried out by hybridizing mRNA isolated from the biological sample or cDNA derived therefrom on a microarray on which a probe specific to at least one marker gene selected from the group consisting of marker genes of Tables 1, 2 and 3 is immobilized to measure a degree of the obtained hybridization. The degree of the hybridization may be measured using an arbitrary measurement method known to those of ordinary skill in the art, such as fluorescence measurement and electrical measurement. In this case, the probe or target nucleic acid may be labeled with a detectable appropriate marker. Herein, the cDNA may be directly amplified by RT-PCR using sense and anti-sense primer pair targeted to at least one marker gene selected from the group consisting of marker genes of Tables 1, 2 and 3 as a primer.

The “measurement of a level of protein” may be conducted using any conventional protein measuring or detecting method. For example, the measurement of a level of protein may be conducted using an analysis method that uses an antibody that specifically binds with protein expressed from at least one marker gene selected from the group consisting of marker genes of Tables 1, 2 and 3. Examples of the protein analysis method using an antibody may include western blotting, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, radioimmunodiffusion, Ouchterlony immunodiffusion, rocket immunoelectrophoresis, immunoprecipitation assay, complement fixation analysis, Fluorescence Activated Cell Sorting (FACS) and the like, but are not limited thereto. Examples of the ELISA include a direct ELISA, an indirect ELISA, a direct sandwich ELISA, an indirect sandwich ELISA and the like. The western blotting is a method in which total protein is isolated and electrophoresized to separate protein according to their size, the separated proteins are then moved into a nitrocellulose membrane to be reacted with an antibody, and a generated amount of the antigen-antibody complex is confirmed using a labeled antibody. In addition, the level of protein may be measured using enzyme, substrate, coenzyme, ligand or the like that specifically binds with the target protein.

The expression level of the marker gene may be determined by measuring an amount of an amplification product obtained by nucleic acid amplification that is carried out by a reverse transcriptase-polymerase chain reaction (RT-PCR) using RNA isolated from the sample as a template.

In addition, the method of predicting a risk of lung cancer recurrence in a lung cancer patient or a patient after a lung cancer treatment includes determining whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group.

The term “recurrence group” refers to a group of patients with lung cancer recurrence within a certain period after a lung cancer treatment among lung cancer patients. Preferably, the term “recurrence group” may refer to a group of patients with lung cancer recurrence within one year after a lung cancer removal operation among lung cancer patients. However, types of lung cancer treatment and a period which is a basis of recurrence may be appropriately adjusted by those of ordinary skill in the art. In addition, the term “non-recurrence group” refers to a group of patients without lung cancer recurrence even after a certain period passes by after a lung cancer treatment among lung cancer patients. Preferably, the term “non-recurrence group” refers to a group of patients without lung cancer recurrence even after three years after a lung cancer removal operation among lung cancer patients. However, types of lung cancer treatment and a period which is a basis of non-recurrence may be appropriately adjusted by those of ordinary skill in the art.

The “expression level of recurrence group” or “expression level of non-recurrence group” corresponds to a standard expression level. Through preliminary experiment, a biological sample of a lung cancer patient, for example, lung cancer tissue is collected in advance. An expression level of at least one marker gene selected from the group consisting of marker genes of Tables 1, 2 and 3 in the lung cancer tissue is then measured. Patients after lung cancer treatment are divided into a recurrence group and a non-recurrence group in which recurrence and non-recurrence respectively occur as time passes by. Next, each of expression levels of the marker gene measured in the recurrence and non-recurrence groups is divided into an expression level of the recurrence group or the non-recurrence group.

The determining whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group may be performed using a statistical forecasting model. In this case, whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group is determined by whether the expression levels show a statistically meaningful difference from each other.

Whether there is a statistically meaningful difference may be determined using a statistical analysis model known to those of ordinary skill in the art. Preferably, the statistical analysis model may be a statistical forecasting model selected from the group consisting of a Linear Discrimination Analysis (LDA) model, a Quadratic Discriminantion Analysis (QDA) prediction model, a Neural Network model, a Decision Tree model, a Support Vector Machine model and a Naive Bayes model, but is not limited thereto.

Examples of the determining whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group include determining to correspond to a non-recurrence group if the expression level of the marker gene shows a statistically meaningful difference from the expression level of the recurrence group, and determining to correspond to a recurrence group if the expression level of the marker gene shows a statistically meaningful difference from the expression level of the non-recurrence group. In addition, examples of the determining whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group include determining to correspond to a recurrence group if the expression level of the marker gene does not show a statistically meaningful difference from the expression level of the recurrence group, and determining to correspond to a non-recurrence group if the expression level of the marker gene does not show a statistically meaningful difference from the expression level of the non-recurrence group.

The statistically meaningful difference may have p values that are statistically meaningfully higher or lower than the expression level of the recurrence group or non-recurrence group. Preferably, the p value may be less than 0.05.

In the method of predicting a risk of lung cancer recurrence in a lung cancer patient or a patient after a lung cancer treatment, if the expression level of the marker gene is determined to correspond to the expression level of the recurrence group, a risk of lung cancer recurrence in a patient can be predicted to be high. In addition, if the expression level of the marker gene is determined to correspond to the expression level of the non-recurrence group, a risk of lung cancer recurrence in a patient can be predicted to be low.

In the method of predicting a risk of lung cancer recurrence in a lung cancer patient or a patient after a lung cancer treatment, specificity may be at least 50%, preferably 60%, more preferably at least 70%, far more preferably at least 80%, and most preferably 90%.

According to another aspect of the present invention, there is provided a method of preparing a report on the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, the method comprising preparing a report representing predicted results according to the method of predicting risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment.

The report may include probability of recurrence according to time.

According to another aspect of the present invention, there is provided a report on a risk of lung cancer recurrence in a lung cancer patient or a patient after a lung cancer treatment, which is prepared by the method of preparing a report on the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment.

According to another aspect of the present invention, there is provided a composition for diagnosing the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, comprising at least one probe or probe set selected from marker genes selected from the group consisting of marker genes of Tables 1, 2 and 3.

The composition may further comprise a reagent required for hybridization reaction with the marker gene in a sample or nucleic acid products expressed therefrom. In addition, the composition may further comprise a buffer, a solvent or the like that stabilizes the probe and acts as a medium of the reaction.

The term “probe” used through the present application refers to a nucleic acid strand that is partially or completely complementary to a target nucleic acid, and refers to oligonucleotide that can bind with the target nucleic acid by a base-specific method. Preferably, the probe may be oligonucleotide that is completely complementary to the target nucleic acid. The probe can be a conventionally known arbitrary nucleic acid derivative that can complementarily bind to the target nucleic acid, such as peptide nucleic acid as well as nucleic acid.

The binding of the probe with the target nucleic acid (in general, referred to as hybridization) may be sequence-dependently carried out under various conditions. In general, the hybridization is performed in a specific ion intensity at specific pH at a temperature that is about 5° C. lower than Tm with respect to a specific sequence. The Tm refers to a state at which 50% of probe complementary to a target sequence is bound to the target sequence. Examples of the conditions of the hybridization may include a pH in the range of 7.0-8.3 and a Na⁺ ion concentration of 0.01-1.0 M. In addition, to raise specificities of the target nucleic acid and the probe, the hybridization may be carried out under conditions that make the binding of the probe with the target nucleic acid unstable, for example, at a high temperature and in the presence of a high concentration of an unstabilizing agent (for example formamide).

The probe may be any length of polynucleotide that can sequence-specifically be bound to the target nucleic acid. For example, the length of the probe may be 7-200 nucleotides, 7-150 nucleotides, 7-100 nucleotides, 7-50 nucleotides, or a full-length strand of gene, but is not limited thereto.

The probe may be labeled with a detectable marker. The detectable marker may be a fluorescent marker such as Cy3 or Cy5, a radioactive material marker, enzyme that converts a substrate to chromogen, or the like, but is not limited thereto.

According to another aspect of the present invention, there is provided a kit for diagnosing the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, comprising at least one probe or probe set selected from marker genes selected from the group consisting of marker genes of Tables 1, 2 and 3.

The probe is the same as defined above. The probe may be labeled with a detectable marker. The detectable marker may be a fluorescent marker such as Cy3 or Cy5, a radioactive material marker, enzyme that converts a substrate to chromogen, or the like, but is not limited thereto.

In the kit, the probe or probe set may be immobilized on a microarray. A target nucleic acid in a sample is hybridized with the probe on the microarray, and the presence and concentration of the target nucleic acid may be determined by measuring the hybridized results. During the hybridization, the target nucleic acid may be labeled with a detectable marker.

The kit may further include a manual that describes a process of measuring a risk of lung cancer recurrence in a lung cancer patient or a patient after a lung cancer treatment.

According to another aspect of the present invention, there is provided a kit for diagnosing the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, comprising sense and anti-sense primer pair with respect to at least one marker gene selected from the group consisting of marker genes of Tables 1, 2 and 3.

The term “primer” used herein refers to a nucleic acid having a free 3′ hydroxy group that is partially or completely complementary to a target nucleic acid and can bind with the template nucleic acid by a sequence-specific method, and refers to oligonucleotide that functions as a starting point for template strand transcription in polymerization.

The kit may further comprise a reagent required for PCR or RT-PCR using the primer described above as a primer and the target nucleic acid as a template. The reagent may include a buffer solution, a DNA polymerase (and/or reverse transcriptase), and 4 types of dNTPs.

The primer may be any length of polynucleotide that can sequence-specifically be bound to the template nucleic acid and function as a starting point for template strand transcription in polymerization. For example, the length of the primer may be 7-200 nucleotides, 7-150 nucleotides, 7-100 nucleotides, 7-50 nucleotides, or a full-length strand of a gene, but is not limited thereto.

The primer may be labeled with a detectable marker. The detectable marker may be a fluorescent marker such as Cy3 or Cy5, a radioactive material marker, enzyme that converts a substrate to chromogen, or the like, but is not limited thereto.

According to another aspect of the present invention, there is provided a microarray for diagnosing a risk of lung cancer recurrence in a lung cancer patient or a patient after a lung cancer treatment, in which at least one probe or probe set selected from marker genes selected from the group consisting of marker genes of Tables 1, 2 and 3.

The term “microarray” refers to a polynucleotide group immobilized on a substrate in a high concentration. The polynucleotide group is respectively immobilized on a certain region. Such microarray is well-known to those of ordinary skill in the art. The microarray is, for example, disclosed in U.S. Pat. Nos. 5,445,934 and 5,744,305, and contents of these patents are included in the present application by reference. The substrate may have various shapes such as plate, film and microsphere (or bead).

The probe is the same as defined above. The probe may be labeled with a detectable marker. The detectable marker may be a fluorescent marker such as Cy3 or Cy5, a radioactive material marker, enzyme that converts a substrate to chromogen, or the like, but is not limited thereto.

The gene expression pattern of the lung cancer cell after lung cancer tissue removal operation is analyzed through a hybridization with the probe on the microarray, and a marker gene that is determined to have a difference in an expression level between a patient with lung cancer recurrence within one year (recurrence group) and a patient without lung cancer recurrence even after three years (non-recurrence group) is selected. The results are shown in Table 1 below. A total number of patients was 60. Among them, the number of patients with lung cancer recurrence within one year after lung cancer tissue removal operation was 19, and the number of patients without lung cancer recurrent even after three years was 41.

TABLE 1 Genbank T-test Fold change NO. Probe Set ID Gene Name Gene Symbol Accession # p-value (abs) 001 1552486_s_at lactamase, beta LACTB NM_171846 0.005162234 1.522293 002 1553105_s_at desmoglein 2 DSG2 NM_001943 0.019467462 2.3323212 003 1553530_a_at integrin, beta 1 (fibronectin receptor, beta polypeptide, ITGB1 NM_033669 0.01684671 1.7791877 antigen CD29 includes MDF2, MSK12) 004 1553678_a_at integrin, beta 1 (fibronectin receptor, beta polypeptide, ITGB1 NM_133376 0.012459265 1.7374801 antigen CD29 includes MDF2, MSK12) 005 1554087_at hypothetical protein FLJ32549 FLJ32549 BC036246 0.002290308 1.5143739 006 1554761_a_at hypothetical protein FLJ20397 FLJ20397 BC010850 0.001210456 1.6267678 007 1555326_a_at ADAM metallopeptidase domain 9 (meltrin gamma) ADAM9 AF495383 0.012324799 2.1980886 008 1555564_a_at I factor (complement) IF BC020718 0.007528743 2.5875902 009 1555705_a_at chemokine-like factor superfamily 3 CKLFSF3 AY168714 0.004961676 1.8587251 010 1557987_at PI-3-kinase-related kinase SMG-1-like locus LOC641298 BC042832 0.010989661 1.7944587 011 1558678_s_at metastasis associated lung adenocarcinoma transcript 1 MALAT1 BE708432 0.00670648 1.6990829 (non-coding RNA) 012 160020_at matrix metallopeptidase 14 (membrane-inserted) MMP14 Z48481 0.005463324 1.5193439 013 200604_s_at protein kinase, cAMP-dependent, regulatory, PRKAR1A M18468 0.017312625 1.5803499 type I, alpha (tissue specific extinguisher 1) 014 200615_s_at adaptor-related protein complex 2, beta 1 subunit AP2B1 AL567295 0.007407852 1.6839108 015 200864_s_at RAB11A, member RAS oncogene family RAB11A NM_004663 0.000163535 1.5653288 034 202267_at laminin, gamma 2 LAMC2 NM_005562 0.004330024 2.8191426 035 202543_s_at glia maturation factor, beta GMFB BC005359 0.008048828 1.5254242 036 202604_x_at ADAM metallopeptidase domain 10 ADAM10 NM_001110 0.002003783 1.767903 037 202627_s_at serpin peptidase inhibitor, clade E (nexin, SERPINE1 AL574210 0.00091248 3.0523725 plasminogen activator inhibitor type 1), member 1 038 202628_s_at serpin peptidase inhibitor, clade E (nexin, SERPINE1 NM_000602 0.00504642 2.6835847 plasminogen activator inhibitor type 1), member 1 039 202817_s_at synovial sarcoma translocation, chromosome 18 SS18 NM_005637 0.005462693 1.5148987 040 202859_x_at interleukin 8 IL8 NM_000584 0.014948112 2.1844351 041 202936_s_at SRY (sex determining region Y)-box 9 SOX9 NM_000346 0.019816045 2.2876046 (campomelic dysplasia, autosomal sex-reversal) 042 202949_s_at four and a half LIM domains 2 FHL2 NM_001450 0.006776552 2.2249734 043 202998_s_at lysyl oxidase-like 2 LOXL2 NM_002318 0.006687925 2.0231075 044 203066_at B cell RAG associated protein GALNAC4S-6ST NM_014863 0.00419499 1.5032523 045 203072_at myosin IE MYO1E NM_004998 0.000449373 1.5877136 046 203293_s_at lectin, mannose-binding, 1 LMAN1 NM_005570 0.002661762 1.9762497 047 203294_s_at lectin, mannose-binding, 1 LMAN1 U09716 0.000473367 1.9764429 048 203414_at monocyte to macrophage differentiation-associated MMD NM_012329 0.001585437 1.6128623 049 203553_s_at mitogen-activated protein kinase kinase kinase kinase 5 MAP4K5 NM_006575 0.010453912 1.5251595 050 203924_at glutathione S-transferase A1 GSTA1 NM_000846 0.004046575 4.2017674 051 203988_s_at fucosyltransferase 8 (alpha (1,6) fucosyltransferase) FUT8 NM_004480 0.01139016 1.6090198 052 204426_at transmembrane emp24 domain trafficking protein 2 TMED2 NM_006815 0.015985437 1.6165011 053 204470_at chemokine (C—X—C motif) ligand 1 CXCL1 NM_001511 0.001788037 3.218731 016 200922_at KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum KDELR1 NM_006801 0.004791257 1.638207 protein retention receptor 1 017 201020_at tyrosine 3-monooxygenase/tryptophan 5-monooxygenase YWHAH NM_003405 0.009279575 1.5148095 activation protein, eta polypeptide 018 201179_s_at guanine nucleotide binding protein (G protein), GNAI3 J03005 0.014834337 1.5069977 alpha inhibiting activity polypeptide 3 019 201309_x_at chromosome 5 open reading frame 13 C5orf13 U36189 0.011555359 2.1326842 020 201363_s_at influenza virus NS1A binding protein IVNS1ABP AB020657 0.00119686 1.5838884 021 201505_at laminin, beta 1 LAMB1 NM_002291 0.000568398 1.8073287 022 201506_at transforming growth factor, beta-induced, 68 kDa TGFBI NM_000358 0.008768089 1.9059453 023 201548_s_at Jumonji, AT rich interactive domain 1B (RBP2-like) JARID1B W02593 0.010550437 1.5276276 024 201559_s_at chloride intracellular channel 4 CLIC4 AF109196 0.002245945 2.1570368 025 201564_s_at fascin homolog 1, actin-bundling protein FSCN1 NM_003088 0.007795681 2.1724482 (Strongylocentrotus purpuratus) 026 201578_at podocalyxin-like PODXL NM_005397 0.00303411 1.8943018 027 201617_x_at caldesmon 1 CALD1 NM_004342 0.01926877 1.8294148 028 201646_at scavenger receptor class B, member 2 SCARB2 AA885297 0.006063032 1.6768507 029 201647_s_at scavenger receptor class B, member 2 SCARB2 NM_005506 0.015885489 1.6841809 030 201695_s_at nucleoside phosphorylase NP NM_000270 0.018524641 1.6833633 031 201722_s_at UDP-N-acetyl-alpha-D-galactosamine:polypeptide GALNT1 AV692127 0.009770202 1.5369248 N-acetylgalactosaminyltransferase 1 (GalNAc-T1) 032 201918_at Solute carrier family 25, member 36 SLC25A36 AI927944 0.00259865 1.6228764 033 201942_s_at carboxypeptidase D CPD D85390 0.017363481 1.7431495 (melanoma growth stimulating activity, alpha) 054 204702_s_at nuclear factor (erythroid-derived 2)-like 3 NFE2L3 NM_004289 0.015985157 1.7023398 055 204790_at SMAD, mothers against DPP homolog 7 (Drosophila) SMAD7 NM_005904 0.013379821 1.7179344 056 204944_at protein tyrosine phosphatase, receptor type, G PTPRG NM_002841 0.004963213 1.769544 057 204989_s_at integrin, beta 4 ITGB4 BF305661 0.012746719 2.1320713 058 205120_s_at sarcoglycan, beta (43 kDa dystrophin-associated glycoprotein) SGCB U29586 0.013908542 1.7317705 059 205180_s_at ADAM metallopeptidase domain 8 ADAM8 NM_001109 0.000473816 2.054043 060 205479_s_at plasminogen activator, urokinase PLAU NM_002658 0.003415823 2.4370956 061 206025_s_at tumor necrosis factor, alpha-induced protein 6 TNFAIP6 AW188195 0.013965369 2.1515768 062 206113_s_at RAB5A, member RAS oncogene family RAB5A NM_004162 0.010821017 1.571063 063 206116_s_at tropomyosin 1 (alpha) TPM1 NM_000366 0.000283653 2.0841253 064 206245_s_at influenza virus NS1A binding protein IVNS1ABP NM_006469 0.003607815 1.5105128 065 206323_x_at oligophrenin 1 OPHN1 NM_002547 0.018292218 1.5056778 066 208510_s_at peroxisome proliferative activated receptor, gamma PPARG NM_015869 0.002361554 1.882336 067 208613_s_at filamin B, beta (actin binding protein 278) FLNB AV712733 0.001033398 1.7958127 068 208637_x_at actinin, alpha 1 ACTN1 BC003576 0.000448714 1.631627 069 208653_s_at CD164 antigen, sialomucin CD164 AF263279 0.017487219 1.5380286 070 208853_s_at calnexin CANX L18887 0.011792572 1.5100785 071 209131_s_at synaptosomal-associated protein, 23 kDa SNAP23 U55936 0.001730693 1.8878508 072 209209_s_at pleckstrin homology domain containing, family C PLEKHC1 AW469573 0.009551367 1.9820172 (with FERM domain) member 1 073 209314_s_at HBS1-like (S. cerevisiae) HBS1L AK024258 0.00507411 1.6641864 074 209316_s_at HBS1-like (S. cerevisiae) HBS1L BC001465 0.006051209 1.6464524 075 209409_at growth factor receptor-bound protein 10 GRB10 DB6962 0.01098607 1.7481923 076 209410_s_at growth factor receptor-bound protein 10 GRB10 AF000017 0.013879589 1.701537 077 209537_at exostoses (multiple)-like 2 EXTL2 AF000416 0.003979554 1.5687809 078 210845_s_at plasminogen activator, urokinase receptor PLAUR U08839 0.007479298 1.7924315 079 210892_s_at general transcription factor II, i GTF2I BC004472 0.003141172 1.619537 080 210933_s_at fascin homolog 1, actin-bundling protein FSCN1 BC004908 0.00342191 1.906748 (Strongylocentrotus purpuratus) 081 210987_x_at tropomyosin 1 (alpha) TPM1 M19267 0.004614187 1.6935222 082 211299_s_at flotillin 2 FLOT2 BC003683 0.015057402 1.5387125 083 211506_s_at interleukin 8 IL8 AF043337 0.005428782 2.867063 084 211559_s_at cyclin G2 CCNG2 L49506 0.010491861 1.8367761 085 211599_x_at met proto-oncogene (hepatocyte growth factor receptor) MET U19348 0.019789577 1.9247686 086 211651_s_at laminin, beta 1 LAMB1 M20206 0.000418344 1.997547 087 211668_s_at plasminogen activator, urokinase PLAU K03226 0.00240352 2.8568754 088 211864_s_at fer-1-like 3, myoferlin (C. elegans) FER1L3 AF207990 0.011889962 1.7860718 089 211924_s_at plasminogen activator, urokinase receptor PLAUR AY029180 0.011789334 1.8189595 090 211981_at collagen, type IV, alpha 1 COL4A1 NM_001845 0.007531395 1.8490748 091 212012_at peroxidasin homolog (Drosophila) PXDN BF342851 0.016265145 1.8463359 092 212660_at PHD finger protein 15 PHF15 AI735639 0.007391165 1.5595657 093 212720_at poly(A) polymerase alpha PAPOLA AI670847 0.016607396 1.5904158 094 212907_at Solute carrier family 30 (zinc transporter), member 1 SLC30A1 AI972416 0.002460855 1.63999 095 213288_at O-acyltransferase (membrane bound) domain containing 2 OACT2 AI761250 0.010427832 1.6232696 096 213457_at malignant fibrous histiocytoma amplified sequence 1 MFHAS1 BF739959 0.003050241 1.8505166 097 213624_at sphingomyelin phosphodiesterase, acid-like 3A SMPDL3A AA873600 0.005912889 1.8562527 098 213742_at splicing factor, arginine/serine-rich 11 SFRS11 AW241752 0.006011819 1.9170463 099 214121_x_at PDZ and LIM domain 7 (enigma) PDLIM7 AA086229 5.50514E−05 1.5048952 100 214196_s_at tripeptidyl peptidase I TPP1 AA602532 0.015398935 1.5939685 101 214544_s_at synaptosomal-associated protein, 23 kDa SNAP23 NM_003825 0.003539713 1.8040004 102 214581_x_at tumor necrosis factor receptor superfamily, member 21 TNFRSF21 BE568134 0.002274355 2.2189345 103 214701_s_at fibronectin 1 FN1 AJ276395 0.001182322 2.071262 104 214866_at plasminogen activator, urokinase receptor PLAUR X74039 0.003173471 1.7340106 105 214895_s_at ADAM metallopeptidase domain 10 ADAM10 AU135154 0.004170008 1.9890832 106 215501_s_at dual specificity phosphatase 10 DUSP10 AK022513 0.018290011 1.5388945 107 216035_x_at transcription factor 7-like 2 (T-cell specific, HMG-box) TCF7L2 AV721430 0.000657631 1.7091621 108 216511_s_at transcription factor 7-like 2 (T-cell specific, HMG-box) TCF7L2 AJ270770 0.004103699 1.5264177 109 216915_s_at protein tyrosine phosphatase, non-receptor type 12 PTPN12 S69182 0.005493577 1.6935816 110 216971_s_at plectin 1, intermediate filament binding protein 500 kDa PLEC1 Z54367 0.01826363 1.7186335 111 217188_s_at chromosome 14 open reading frame 1 C14orf1 AC007182 0.011925477 1.6185476 112 217448_s_at chromosome 14 open reading frame 92 C14orf92 AL117508 0.007782524 1.5433311 similar to Epidermal Langerhans cell protein LCP1 LOC285412 113 217492_s_at phosphatase and tensin homolog PTEN AF023139 0.007220107 1.5624946 (mutated in multiple advanced cancers 1) 114 218000_s_at pleckstrin homology-like domain, family A, member 1 PHLDA1 NM_007350 0.016502094 1.6960312 115 218077_s_at zinc finger, DHHC-type containing 3 ZDHHC3 BE542551 0.01684034 1.5417765 116 218078_s_at zinc finger, DHHC-type containing 3 ZDHHC3 NM_016598 0.010970607 1.5836283 117 218435_at DnaJ (Hsp40) homolog, subfamily C, member 15 DNAJC15 NM_013238 0.019865552 1.7292447 118 218644_at pleckstrin 2 PLEK2 NM_016445 0.000675608 2.7071812 119 218748_s_at SEC10-like 1 (S. cerevisiae) SEC10L1 NM_006544 0.012352341 1.7368068 120 218815_s_at transmembrane protein 51 TMEM51 NM_018022 0.000753902 1.6477742 121 218826_at solute carrier family 35, member F2 SLC35F2 NM_017515 0.009280122 1.6340361 122 218854_at squamous cell carcinoma SART2 NM_013352 0.014419112 1.6285655 antigen recognized by T cells 2 123 218856_at tumor necrosis factor receptor superfamily, member 21 TNFRSF21 NM_016629 0.01292243 1.617686 124 218885_s_at UDP-N-acetyl-alpha-D-galactosamine:polypeptide GALNT12 NM_024642 0.014052196 1.6402073 N-acetylgalactosaminyltransferase 12 (GalNAc-T12) 125 219410_at transmembrane protein 45A TMEM45A NM_018004 0.018847797 2.0938365 126 219603_s_at zinc finger protein 226 ZNF226 NM_015919 0.005593323 1.5408667 127 220199_s_at chromosome 1 open reading frame 80 C1orf80 NM_022831 0.016323 1.5315142 128 220617_s_at zinc finger protein 532 ZNF532 NM_018181 0.001976648 1.5441327 129 221268_s_at sphingosine-1-phosphate phosphatase 1 SGPP1 NM_030791 0.008873873 1.9432548 130 221881_s_at chloride intracellular channel 4 CLIC4 AI638420 0.004401053 1.7742935 131 222399_s_at SM-11044 binding protein SMBP BG104571 0.00011337 1.5270268 132 222449_at transmembrane, prostate TMEPAI AL035541 0.005303006 2.2757804 androgen induced RNA 133 222528_s_at solute carrier family 25, member 37 SLC25A37 BG251467 0.014745607 1.738053 134 222540_s_at hepatitis B virus x associated protein HBXAP BG286920 0.005694628 1.5068418 135 222692_s_at fibronectin type III domain containing 3B FNDC3B BF444916 0.001075083 1.5835624 136 222693_at fibronectin type III domain containing 3B FNDC3B BF444916 0.000622161 1.7766397 137 222773_s_at UDP-N-acetyl-alpha-D-galactosamine:polypeptide GALNT12 AA554045 0.003090952 1.8790901 N-acetylgalactosaminyltransferase 12 (GalNAc-T12) 138 223577_x_at PRO1073 protein PRO1073 AA827878 0.003659447 1.6790042 139 223940_x_at metastasis associated lung adenocarcinoma MALAT1 AF132202 0.016841894 1.9524238 transcript 1 (non-coding RNA) 140 224558_s_at metastasis associated lung adenocarcinoma MALAT1 AI446756 0.012874936 1.6367766 transcript 1 (non-coding RNA) 141 224674_at tweety homolog 3 (Drosophila) TTYH3 AI934753 0.002428954 1.6452742 142 224733_at chemokine-like factor superfamily 3 CKLFSF3 AL574900 0.013543638 1.5199631 143 224802_at Nedd4 family interacting protein 2 NDFIP2 AA019338 0.013437813 1.5261155 144 225021_at zinc finger protein 532 ZNF532 AA861416 0.002285053 1.6213596 145 225140_at Kruppel-like factor 3 (basic) KLF3 BF438116 0.016804362 1.5368354 146 225168_at FERM domain containing 4A FRMD4A T78406 0.006987929 1.5712297 147 225424_at glycerol-3-phosphate acyltransferase, mitochondrial GPAM AB046780 0.000390623 1.7006425 148 225503_at dehydrogenase/reductase (SDR family) X-linked DHRSX AL547782 0.005000754 1.770981 149 225567_at Hypothetical LOC388114 LOC388114 BE207755 0.003047524 1.6990312 150 225609_at glutathione reductase GSR AI888037 0.004693668 1.8490914 151 225842_at Pleckstrin homology-like domain, family A, member 1 PHLDA1 AK026181 0.014052763 1.8735564 152 226084_at microtubule-associated protein 1B MAP1B AA554833 0.016480966 1.9064581 153 226352_at Junction-mediating and regulatory protein JMY BF447037 0.001219355 1.5196482 154 226726_at O-acyltransferase (membrane bound) domain containing 2 OACT2 W63676 0.005363467 1.8277074 155 226780_s_at hypothetical protein HSPC268 HSPC268 BF540829 0.001859941 1.5185972 156 227257_s_at chromosome 10 open reading frame 46 C10orf46 AW973842 0.000646104 1.6094143 157 227628_at similar to RIKEN cDNA 2310016C16 LOC493869 AL571557 0.006222301 2.0978951 158 227808_at DnaJ (Hsp40) homolog, subfamily C, member 15 DNAJC15 AI091398 0.01153802 1.7936606 159 230206_at Dedicator of cytokinesis 5 DOCK5 AI692645 0.005127667 1.6694399 160 231735_s_at PRO1073 protein PRO1073 NM_014086 0.004784999 1.72546 161 231823_s_at KIAA1295 KIAA1295 BG054798 0.002478401 1.5713933 162 235587_at hypothetical protein LOC202781 LOC202781 BG400596 0.018314553 1.5202585 163 235879_at Muscleblind-like (Drosophila) MBNL1 AI697540 0.002645486 2.0540323 164 238558_at Muscleblind-like (Drosophila) MBNL1 AI445833 0.004576562 1.805269 165 238563_at Ab1-interactor 1 ABI1 AV762916 0.012934915 1.6069295 166 238701_x_at FLJ45803 protein FLJ45803 BE176566 0.01719282 1.5133282 The gene expression pattern of the lung cancer cell classified into adenocarcinoma after lung cancer tissue removal operation is analyzed through a hybridization with the probe on the microarray, and a marker gene that is determined to have a difference in an expression level between a patient with lung cancer recurrence within one year (recurrence group) and a patient without lung cancer recurrence even after three years (non-recurrence group) is selected. The results are shown in Table 2 below. A total number of adenocarcinoma patients was 23. Among them, the number of patients with lung cancer recurrence within one year after lung cancer tissue removal operation was 8, and the number of patients without lung cancer recurrent even after three years was 15.

The gene expression pattern of the lung cancer cell classified into squamous cell carcinoma after lung cancer tissue removal operation is analyzed through a hybridization with the probe on the microarray, and a marker gene that is determined to have a difference in an expression level between a patient with lung cancer recurrence within one year (recurrence group) and a patient without lung cancer recurrence even after three years (non-recurrence group) is selected. The results are shown in Table 3 below. A total number of squamous cell carcinoma patients was 37. Among them, the number of patients with lung cancer recurrence within one year after lung cancer tissue removal operation was 11, and the number of patients without lung cancer recurrent even after three years was 26.

TABLE 2 Genbank T-test Fold change NO. Probe Set ID Gene Name Gene Symbol Accession # p-value (abs) 001 1553105_s_at desmoglein 2 DSG2 NM_001943 0.01 5.339528 002 1553589_a_at PDZK1 interacting protein 1 PDZK1IP1 NM_005764 0.02 3.608417 003 1553768_a_at discoidin, CUB and LCCL domain containing 1 DCBLD1 NM_173674 0.01 1.9046342 004 1553928_at ELMO domain containing 2 ELMOD2 NM_153702 0.02 1.7168769 005 1554327_a_at calcium activated nucleotidase 1 CANT1 AF328554 0.02 1.6306834 006 1558685_a_at hypothetical protein BC009467 LOC158980 BC009467 0.03 1.6841992 007 1559399_s_at zinc finger, CCHC domain containing 10 ZCCHC10 BC015988 0.02 1.5219704 008 1568578_s_at FGFR1 oncogene partner FGFR1OP BC037785 0.01 2.4856193 009 160020_at matrix metallopeptidase 14 (membrane-inserted) MMP14 Z48481 0.03 1.8354192 010 200730_s_at protein tyrosine phosphatase type IVA, member 1 PTP4A1 BF576710 0.03 2.6575127 011 200733_s_at protein tyrosine phosphatase type IVA, member 1 PTP4A1 U48296 0.02 1.5593889 012 200864_s_at RAB11A, member RAS oncogene family RAB11A NM_004663 0.02 1.6270655 013 200890_s_at signal sequence receptor, alpha SSR1 AW006345 0.01 1.8127153 (translocon-associated protein alpha) 014 200931_s_at vinculin VCL NM_014000 0.01 1.7692009 015 201011_at ribophorin I RPN1 NM_002950 0.01 1.6075972 016 201106_at glutathione peroxidase 4 GPX4 NM_002085 0.02 1.6833277 (phospholipid hydroperoxidase) 017 201143_s_at eukaryotic translation initiation factor 2 EIF2S1 BC002513 0.02 2.298374 subunit 1 alpha, 35 kDa 018 201207_at tumor necrosis factor, alpha-induced protein 1 (endothelial) TNFAIP1 NM_021137 0.01 1.6828994 019 201250_s_at solute carrier family 2 SLC2A1 NM_006516 0.02 4.009399 (facilitated glucose transporter), member 1 020 201392_s_at insulin-like growth factor 2 receptor IGF2R BG031974 0.02 1.6488191 021 201393_s_at insulin-like growth factor 2 receptor IGF2R NM_000876 0.02 1.5784883 022 201456_s_at BUB3 budding uninhibited by BUB3 AU160695 0.01 1.7238452 benzimidazoles 3 homolog (yeast) 023 201458_s_at BUB3 budding uninhibited by BUB3 NM_004725 0.01 1.5530633 benzimidazoles 3 homolog (yeast) 024 201525_at apolipoprotein D APOD NM_001647 0.03 4.186704 025 201564_s_at fascin homolog 1, actin-bundling protein FSCN1 NM_003088 0.01 3.2328043 (Strongylocentrotus purpuratus) 026 201631_s_at immediate early response 3 IER3 NM_003897 0.01 3.0016828 027 201656_at integrin, alpha 6 ITGA6 NM_000210 0.01 2.3616688 028 201700_at cyclin D3 CCND3 NM_001760 0.02 1.6460308 029 202047_s_at chromobox homolog 6 CBX6 AI458128 0.01 1.9611783 030 202048_s_at chromobox homolog 6 CBX6 NM_014292 0.02 1.6010046 031 202086_at myxovirus (influenza virus) resistance 1, MX1 NM_002462 0.02 2.4754105 interferon-inducible protein p78 (mouse) 032 202130_at RIO kinase 3 (yeast) RIOK3 AA725102 0.01 1.6167943 033 202131_s_at RIO kinase 3 (yeast) RIOK3 NM_003831 0.02 1.7833867 034 202233_s_at ubiquinol-cytochrome c reductase hinge protein UQCRH NM_006004 0.03 1.5353662 035 202267_at laminin, gamma 2 LAMC2 NM_005562 0.01 3.9229517 036 202293_at stromal antigen 1 STAG1 AW168948 0.01 1.7993419 037 202604_x_at ADAM metallopeptidase domain 10 ADAM10 NM_001110 0.02 2.0231702 038 202696_at oxidative-stress responsive 1 OXSR1 NM_005109 0.03 1.5418515 039 202816_s_at synovial sarcoma translocation, chromosome 18 SS18 AW292882 0.01 2.0899003 040 202856_s_at solute carrier family 16 (monocarboxylic acid transporters), SLC16A3 NM_004207 0.01 2.8914852 member 3 041 202869_at 2′,5′-oligoadenylate synthetase 1, 40/46 kDa OAS1 NM_016816 0.02 3.431309 042 202887_s_at DNA-damage-inducible transcript 4 DDIT4 NM_019058 0.02 2.74081 043 202904_s_at LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) LSM5 NM_012322 0.03 1.8907431 044 202934_at hexokinase 2 HK2 AI761561 0.01 2.1517375 045 203072_at myosin IE MYO1E NM_004998 0.01 2.039332 046 203177_x_at transcription factor A, mitochondrial TFAM NM_003201 0.02 1.8601428 047 203256_at cadherin 3, type 1, P-cadherin (placental) CDH3 NM_001793 0.01 2.6757588 048 203287_at ladinin 1 LAD1 NM_005558 0.03 1.9237865 049 203311_s_at ADP-ribosylation factor 6 ARF6 M57763 0.02 1.9452083 050 203313_s_at TGFB-induced factor (TALE family homeobox) TGIF NM_003244 0.01 1.5528815 051 203344_s_at retinoblastoma binding protein 8 RBBP8 NM_002894 0.01 1.7286093 052 203395_s_at hairy and enhancer of split 1, (Drosophila) HES1 NM_005524 0.02 1.6101321 053 203430_at heme binding protein 2 HEBP2 NM_014320 0.02 1.822933 054 203476_at trophoblast glycoprotein TPBG NM_006670 0.03 2.0313597 055 203499_at EPH receptor A2 EPHA2 NM_004431 0.01 2.4758015 056 203501_at plasma glutamate carboxypeptidase PGCP NM_006102 0.02 1.742001 057 203535_at S100 calcium binding protein A9 (calgranulin B) S100A9 NM_002965 0.02 5.647521 058 203554_x_at pituitary tumor-transforming 1 PTTG1 NM_004219 0.02 2.1384234 059 203642_s_at COBL-like 1 COBLL1 NM_014900 0.02 1.7199888 060 203690_at tubulin, gamma complex associated protein 3 TUBGCP3 NM_006322 0.01 1.6228286 061 203906_at IQ motif and Sec7 domain 1 IQSEC1 AI652645 0.01 1.7168043 062 203964_at N-myc (and STAT) interactor NMI NM_004688 0.01 1.8720082 063 203988_s_at fucosyltransferase 8 (alpha (1,6) fucosyltransferase) FUT8 NM_004480 0.01 2.0948534 064 204136_at collagen, type VII, alpha 1 (epidermolysis bullosa, COL7A1 NM_000094 0.01 2.2071517 dystrophic, dominant and recessive) 065 204401_at potassium intermediate/small conductance KCNN4 NM_002250 0.01 3.260382 calcium-activated channel, subfamily N, member 4 066 204415_at interferon, alpha-inducible protein (clone IFI-6-16) G1P3 NM_022873 0.02 4.0747566 067 204470_at chemokine (C—X—C motif) ligand 1 CXCL1 NM_001511 0.01 6.7313213 (melanoma growth stimulating activity, alpha) 068 204580_at matrix metallopeptidase 12 (macrophage elastase) MMP12 NM_002426 0.02 7.360193 069 204587_at solute carrier family 25 (mitochondrial carrier, brain), member 14 SLC25A14 NM_003951 0.02 1.5086871 070 204616_at ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase) UCHL3 NM_006002 0.03 1.8766123 071 204635_at ribosomal protein S6 kinase, 90 kDa, polypeptide 5 RPS6KA5 NM_004755 0.01 1.853935 072 204747_at interferon-induced protein with tetratricopeptide repeats 3 IFIT3 NM_001549 0.02 2.588765 073 204809_at ClpX caseinolytic peptidase X homolog (E. coli) CLPX NM_006660 0.02 1.5264844 074 204857_at MAD1 mitotic arrest deficient-like 1 (yeast) MAD1L1 NM_003550 0.03 1.6594671 075 204875_s_at GDP-mannose 4,6-dehydratase GMDS NM_001500 0.02 2.5758607 076 204990_s_at integrin, beta 4 ITGB4 NM_000213 0.01 3.176456 077 205004_at NF-kappaB repressing factor NKRF NM_017544 0.02 1.5878501 078 205016_at transforming growth factor, alpha TGFA NM_003236 0.01 2.1914852 079 205120_s_at sarcoglycan, beta (43 kDa dystrophin-associated glycoprotein) SGCB U29586 0.01 2.5721073 080 205157_s_at keratin 17 KRT17 NM_000422 0.01 5.252511 081 205180_s_at ADAM metallopeptidase domain 8 ADAM8 NM_001109 0.01 2.1361954 082 205202_at protein-L-isoaspartate (D-aspartate) O-methyltransferase PCMT1 NM_005389 0.01 1.5924072 083 205339_at TAL1 (SCL) interrupting locus SIL NM_003035 0.02 2.043193 084 205455_at macrophage stimulating 1 receptor (c-met-related tyrosine kinase) MST1R NM_002447 0.02 2.835629 085 205479_s_at plasminogen activator, urokinase PLAU NM_002658 0.01 3.8200433 086 205518_s_at cytidine monophosphate-N-acetylneuraminic acid CMAH NM_003570 0.01 2.596108 hydroxylase (CMP-N-acetylneuraminate monooxygenase) 087 205945_at interleukin 6 receptor IL6R NM_000565 0.03 1.8261979 088 206055_s_at small nuclear ribonucleoprotein polypeptide A′ SNRPA1 NM_003090 0.01 1.5232844 089 206323_x_at oligophrenin 1 OPHN1 NM_002547 0.01 2.3268037 090 206414_s_at development and differentiation enhancing factor 2 DDEF2 NM_003887 0.01 2.089077 091 207079_s_at mediator of RNA polymerase II transcription, MED6 NM_005466 0.03 1.8905708 subunit 6 homolog (yeast) 092 207850_at chemokine (C—X—C motif) ligand 3 CXCL3 NM_002090 0.02 4.294934 093 208091_s_at EGFR-coamplified and overexpressed protein ECOP NM_030796 0.02 2.2340379 094 208613_s_at filamin B, beta (actin binding protein 278) FLNB AV712733 0.01 2.3647172 095 208636_at Actinin, alpha 1 ACTN1 AI082078 0.01 1.8102713 096 208637_x_at actinin, alpha 1 ACTN1 BC003576 0.01 2.062581 097 208819_at RAB8A, member RAS oncogene family RAB8A BC002977 0.01 1.6729795 098 208840_s_at Ras-GTPase activating protein G3BP2 AU149503 0.02 1.8072606 SH3 domain-binding protein 2 099 208875_s_at p21 (CDKN1A)-activated kinase 2 PAK2 BF796470 0.01 2.1095228 100 208876_s_at p21 (CDKN1A)-activated kinase 2 PAK2 AI076186 0.02 1.6706929 101 208878_s_at p21 (CDKN1A)-activated kinase 2 PAK2 AF092132 0.02 1.5662557 102 209022_at stromal antigen 2 STAG2 AK026678 0.01 1.5019888 103 209025_s_at synaptotagmin binding, cytoplasmic RNA interacting protein SYNCRIP AF037448 0.01 1.748127 104 209314_s_at HBS1-like (S. cerevisiae) HBS1L AK024258 0.01 2.2400491 105 209417_s_at interferon-induced protein 35 IFI35 BC001356 0.02 1.9908478 106 209476_at thioredoxin domain containing TXNDC AL080080 0.02 1.5641398 107 209487_at RNA binding protein with multiple splicing RBPMS D84109 0.02 1.5929683 108 209537_at exostoses (multiple)-like 2 EXTL2 AF000416 0.03 2.019564 109 209627_s_at oxysterol binding protein-like 3 OSBPL3 AY008372 0.03 1.9842228 110 209791_at peptidyl arginine deiminase, type II PADI2 AL049569 0.02 1.5902214 111 210092_at mago-nashi homolog, MAGOH AF067173 0.03 1.7290384 proliferation-associated (Drosophila) 112 210093_s_at mago-nashi homolog, proliferation-associated (Drosophila) MAGOH AF067173 0.01 1.5214177 113 210104_at mediator of RNA polymerase II transcription, MED6 AF074723 0.01 1.7416326 subunit 6 homolog (yeast) 114 210273_at BH-protocadherin (brain-heart) PCDH7 AB006757 0.03 1.5068512 115 210933_s_at fascin homolog 1, actin-bundling protein FSCN1 BC004908 0.01 2.660472 (Strongylocentrotus purpuratus) 116 211160_x_at actinin, alpha 1 ACTN1 M95178 0.01 1.6758434 117 211668_s_at plasminogen activator, urokinase PLAU K03226 0.03 4.548989 118 211737_x_at pleiotrophin PTN BC005916 0.02 2.2613049 (heparin binding growth factor 8, neurite growth-promoting factor 1) 119 212203_x_at interferon induced transmembrane protein 3 (1-8U) IFITM3 BF338947 0.01 1.5134683 120 212221_x_at iduronate 2-sulfatase (Hunter syndrome) IDS AV703259 0.01 1.8884305 121 212236_x_at keratin 17 KRT17 Z19574 0.01 3.7909358 122 212268_at serpin peptidase inhibitor, clade B (ovalbumin), member 1 SERPINB1 NM_030666 0.02 1.9949495 123 212312_at BCL2-like 1 BCL2L1 AL117381 0.02 1.5705433 124 212322_at sphingosine-1-phosphate lyase 1 SGPL1 BE999972 0.01 1.6549215 125 212330_at transcription factor Dp-1 TFDP1 R60866 0.02 2.1620867 126 212531_at lipacalin 2 (oncogene 24p3) LCN2 NM_005564 0.02 6.2857018 127 212657_s_at interleukin 1 receptor antagonist IL1RN U65590 0.02 3.7755005 128 212858_at progestin and adipoQ receptor family member IV PAQR4 AL520675 0.01 2.2580597 129 212992_at chromosome 14 open reading frame 78 C14orf78 AI935123 0.01 5.9573503 130 213088_s_at DnaJ (Hsp40) homolog, subfamily C, member 9 DNAJC9 BE551340 0.02 1.784215 131 213288_at O-acyltransferase (membrane bound) domain containing 2 OACT2 AI761250 0.02 2.1144574 132 214121_x_at PDZ and LIM domain 7 (enigma) PDLIM7 AA086229 0.01 1.7699668 133 214453_s_at interferon-induced protein 44 IFI44 NM_006417 0.03 2.8858101 134 214697_s_at ROD1 regulator of differentiation 1 (S. pombe) ROD1 AW190873 0.01 2.048636 135 214974_x_at chemokine (C—X—C motif) ligand 5 CXCL5 AK026546 0.02 6.4936213 136 215223_s_at superoxide dismutase 2, mitochondrial SOD2 W46388 0.01 3.1782749 137 215230_x_at eukaryotic translation initiation factor 3, subunit 8, 110 kDa EIF3S8 AA679705 0.02 1.6019442 138 215411_s_at TRAF3 interacting protein 2 TRAF3IP2 AL008730 0.03 1.72815 139 216153_x_at reversion-inducing-cysteine-rich RECK AK022897 0.01 1.9417262 protein with kazal motifs 140 216841_s_at superoxide dismutase 2, mitochondrial SOD2 X15132 0.01 2.8182118 141 216905_s_at suppression of tumorigenicity 14 ST14 U20428 0.02 1.8127093 (colon carcinoma, matriptase, epithin) 142 216977_x_at small nuclear ribonucleoprotein polypeptide A′ SNRPA1 AJ130972 0.01 1.5991035 143 217834_s_at synaptotagmin binding, cytoplasmic RNA interacting protein SYNCRIP NM_006372 0.03 1.7178055 144 217867_x_at beta-site APP-cleaving enzyme 2 BACE2 NM_012105 0.01 2.5611665 145 217901_at Desmoglein 2 DSG2 BF031829 0.01 3.4549432 146 218012_at TSPY-like 2 TSPYL2 NM_022117 0.01 1.6316599 147 218288_s_at hypothetical protein MDS025 MDS025 NM_021825 0.01 1.7013886 148 218294_s_at nucleoporin 50 kDa NUP50 AF267865 0.01 1.5833666 149 218400_at 2′-5′-oligoadenylate synthetase 3, 100 kDa OAS3 NM_006187 0.01 3.0217175 150 218451_at CUB domain containing protein 1 CDCP1 NM_022842 0.01 3.0102131 151 218460_at hypothetical protein FLJ20397 FLJ20397 NM_017802 0.02 1.6881874 152 218498_s_at ERO1-like (S. cerevisiae) ERO1L NM_014584 0.01 2.5205412 153 218573_at melanoma antigen family H, 1 MAGEH1 NM_014061 0.02 1.6212198 154 218585_s_at denticleless homolog (Drosophila) DTL NM_016448 0.03 2.4223747 155 218644_at pleckstrin 2 PLEK2 NM_016445 0.01 4.898943 156 218796_at chromosome 20 open reading frame 42 C20orf42 NM_017671 0.02 3.3694396 157 218826_at solute carrier family 35, member F2 SLC35F2 NM_017515 0.03 2.0183008 158 218943_s_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 DDX58 NM_014314 0.02 2.4575703 159 218950_at centaurin, delta 3 CENTD3 NM_022481 0.02 1.5173771 160 219146_at chromosome 17 open reading frame 42 C17orf42 NM_024683 0.02 1.5234692 161 219296_at zinc finger, DHHC-type containing 13 ZDHHC13 NM_019028 0.03 1.5033884 162 219303_at chromosome 13 open reading frame 7 C13orf7 NM_024546 0.03 1.5534021 163 219332_at MICAL-like 2 MICAL-L2 NM_024723 0.02 1.8410143 164 219399_at lin-7 homolog C (C. elegans) LIN7C NM_018362 0.03 1.5852816 165 219421_at osmosis responsive factor OSRF NM_012382 0.01 1.531867 166 219439_at core 1 synthase, glycoprotein-N-acetylgalactosamine C1GALT1 NM_020156 0.02 2.2143774 3-beta-galactosyltransferase, 1 167 219517_at elongation factor RNA polymerase II-like 3 ELL3 NM_025165 0.02 1.6594616 168 219549_s_at reticulon 3 RTN3 NM_006054 0.02 1.6491096 169 219603_s_at zinc finger protein 226 ZNF226 NM_015919 0.01 1.8911394 170 219630_at PDZK1 interacting protein 1 PDZK1IP1 NM_005764 0.02 3.5720232 171 219691_at sterile alpha motif domain containing 9 SAMD9 NM_017654 0.01 2.2009485 172 219787_s_at epithelial cell transforming sequence 2 oncogene ECT2 NM_018098 0.02 3.414079 173 219799_s_at dehydrogenase/reductase (SDR family) member 9 DHRS9 NM_005771 0.02 1.7866958 174 219959_at molybdenum cofactor sulfurase MOCOS NM_017947 0.01 3.192601 175 220232_at stearoyl-CoA desaturase 5 SCD5 NM_024906 0.01 3.2719014 176 220368_s_at KIAA2010 KIAA2010 NM_017936 0.02 1.6052217 177 220725_x_at Dynein, axonemal, heavy polypeptide 3 DNAH3 NM_025095 0.01 1.8525391 178 221477_s_at hypothetical protein MGC5618 MGC5618 BF575213 0.01 2.2014346 179 221482_s_at cyclic AMP phosphoprotein, 19 kD ARPP-19 BC003418 0.02 1.711658 180 221732_at calcium activated nucleotidase 1 CANT1 AK026161 0.02 1.6711121 181 221752_at Slingshot homolog 1 (Drosophila) SSH1 AL041728 0.02 1.678051 182 221922_at G-protein signalling modulator 2 (AGS3-like, C. elegans) GPSM2 AW195581 0.01 2.2638144 183 222392_x_at PERP, TP53 apoptosis effector PERP AJ251830 0.02 1.8814404 184 222399_s_at SM-11044 binding protein SMBP BG104571 0.02 1.6986449 185 222424_s_at nuclear casein kinase and cyclin-dependent kinase substrate 1 NUCKS1 BC000805 0.01 1.6469624 186 222446_s_at beta-site APP-cleaving enzyme 2 BACE2 AF178532 0.01 1.9711965 187 222492_at pyridoxal (pyridoxine, vitamin B6) kinase PDXK AW262867 0.01 1.5873553 188 222502_s_at ubiquitin-fold modifier 1 UFM1 BC005193 0.02 1.7238611 189 222523_at SUMO1/sentrin/SMT3 specific peptidase 2 SENP2 BE622841 0.03 1.7830018 190 222528_s_at solute carrier family 25, member 37 SLC25A37 BG251467 0.02 2.6761055 191 222561_at LanC lantibiotic synthetase component C-like 2 (bacterial) LANCL2 AJ278245 0.03 2.2797666 192 222587_s_at UDP-N-acetyl-alpha-D-galactosamine: polypeptide GALNT7 BF699855 0.03 1.7439753 N-acetylgalactosaminyltransferase 7(GalNAc-T7) 193 222689_at phytoceramidase, alkaline PHCA N51263 0.01 1.7877864 194 222692_s_at fibronectin type III domain containing 3B FNDC3B BF444916 0.01 1.9685304 195 222693_at fibronectin type III domain containing 3B FNDC3B BF444916 0.02 2.1501522 196 222793_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 DDX58 AK023661 0.01 2.2502613 197 223219_s_at CCR4-NOT transcription complex, subunit 10 CNOT10 BC002931 0.01 1.5173706 198 223278_at gap junction protein, beta 2, 26 kDa (connexin 26) GJB2 M86849 0.02 5.1083236 199 223374_s_at UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 B3GALT3 AF154848 0.02 2.124231 200 223421_at cysteine/histidine-rich 1 CYHR1 BC005073 0.01 1.7838429 201 223467_at RAS, dexamethasone-induced 1 RASD1 AF069506 0.01 3.1274104 202 223626_x_at family with sequence similarity 14, member A FAM14A AF208232 0.01 1.5701514 203 223631_s_at chromosome 19 open reading frame 33 C19orf33 AF213678 0.02 3.90325 204 224159_x_at tripartite motif-containing 4 TRIM4 AF220023 0.01 2.2881489 205 224493_x_at chromosome 18 open reading frame 45 C18orf45 BC006280 0.02 1.571958 206 224494_x_at dehydrogenase/reductase (SDR family) member 10 DHRS10 BC006283 0.02 1.9102337 207 224564_s_at reticulon 3 RTN3 BE544689 0.01 1.583082 208 224595_at solute carrier family 44, member 1 SLC44A1 AK022549 0.01 1.601491 209 224596_at solute carrier family 44, member 1 SLC44A1 AI634866 0.01 1.5728544 210 224598_at mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N- MGAT4B BF570193 0.03 1.5535489 acetylglucosaminyltransferase, isoenzyme B 211 224674_at tweety homolog 3 (Drosophila) TTYH3 AI934753 0.02 2.123153 212 224675_at mesoderm development candidate 2 MESDC2 AK026606 0.01 1.6605617 213 224679_at mesoderm development candidate 2 MESDC2 BE963495 0.01 1.65804 214 224681_at guanine nucleotide binding protein (G protein) alpha 12 GNA12 BG028884 0.01 1.6103705 215 224799_at Nedd4 family interacting protein 2 NDFIP2 AW290956 0.02 1.9774225 216 224802_at Nedd4 family interacting protein 2 NDFIP2 AA019338 0.02 1.6960912 217 224827_at Dendritic cell-derived ubiquitin-like protein DC-UbP AK022894 0.01 1.5073498 218 224902_at pyruvate dehydrogenase phosphatase regulatory subunit PDPR BE644918 0.02 1.6357323 219 224950_at prostaglandin F2 receptor negative regulator PTGFRN BF476250 0.03 1.9777663 220 225071_at chromosome 6 open reading frame 68 C6orf68 BG168247 0.03 1.6909997 221 225272_at spermidine/spermine N1-acetyltransferase 2 SAT2 AA128261 0.01 1.6911607 222 225331_at chromosome 3 open reading frame 6 C3orf6 BF941088 0.02 2.126105 223 225342_at adenylate kinase 3-like 1 AK3L1 AK026966 0.01 7.1160383 224 225366_at phosphoglucomutase 2 PGM2 AI652855 0.03 1.527827 225 225375_at chromosome 17 open reading frame 32 C17orf32 AW975808 0.02 1.8780395 226 225380_at hypothetical protein BC007901 LOC91461 BF528878 0.02 2.6365216 227 225383_at zinc finger protein 275 ZNF275 BF793625 0.01 1.639558 228 225547_at HBII-276 host gene HBII-276HG BG169443 0.01 1.6269366 229 225550_at AV700816 0.01 1.6167612 230 225571_at leukemia inhibitory factor receptor LIFR AA701657 0.03 3.5799398 231 225575_at leukemia inhibitory factor receptor LIFR AI680541 0.01 3.1433964 232 225578_at similar to RIKEN cDNA 2410129H14 LOC440145 AI885466 0.01 1.8692675 233 225750_at ERO1-like (S. cerevisiae) ERO1L BE966748 0.02 2.0413787 234 225842_at Pleckstrin homology-like domain, family A, member 1 PHLDA1 AK026181 0.02 2.5619717 235 225847_at arylacetamide deacetylase-like 1 AADACL1 AB037784 0.02 1.6796919 236 226060_at RFT1 homolog (S. cerevisiae) RFT1 BF475369 0.02 1.5211235 237 226112_at sarcoglycan, beta (43 kDa dystrophin-associated glycoprotein) SGCB AI678717 0.01 1.5416645 238 226278_at hypothetical protein DKFZp313A2432 DKFZp313A2432 AI150224 0.02 1.6910942 239 226335_at ribosomal protein S6 kinase, 90 kDa, polypeptide 3 RPS6KA3 BG498334 0.01 1.8176109 240 226352_at Junction-mediating and regulatory protein JMY BF447037 0.01 2.4128768 241 226488_at RCC1 domain containing 1 RCCD1 AW007826 0.03 1.777583 242 226568_at hypothetical protein LOC284611 LOC284611 AI478747 0.01 2.1426997 243 226609_at discoidin, CUB and LCCL domain containing 1 DCBLD1 N22751 0.01 2.0089936 244 226702_at hypothetical protein LOC129607 LOC129607 AI742057 0.01 2.5539525 245 226722_at family with sequence similarity 20, member C FAM20C BE874872 0.01 2.2937167 246 226726_at O-acyltransferase (membrane bound) domain containing 2 OACT2 W63676 0.01 2.8518102 247 226778_at Chromosome 8 open reading frame 42 C8orf42 AI632224 0.02 1.9250498 248 226780_s_at hypothetical protein HSPC268 HSPC268 BF540829 0.01 1.8384567 249 226781_at hypothetical protein HSPC268 HSPC268 BF540829 0.01 1.7917764 250 226784_at TWIST neighbor TWISTNB AA121481 0.01 1.750498 251 226832_at Hypothetical LOC389188 LOC389188 BF978778 0.01 1.538109 252 226863_at Full-length cDNA clone CS0DJ001YJ05 of T cells AI674565 0.01 3.1555974 (Jurkat cell line) Cot 10-normalized of Homo sapiens (human) 253 226926_at dermokine ZD52F10 AA706316 0.02 3.190141 254 227141_at chromosome 1 open reading frame 171 C1orf171 AW205739 0.02 1.6063374 255 227148_at pleckstrin homology domain containing, family H PLEKHH2 AI913749 0.03 2.1525955 (with MyTH4 domain) member 2 256 227172_at hypothetical protein BC000282 LOC89894 BC000282 0.02 1.9858925 257 227249_at AI857685 0.01 1.9229563 258 227314_at Integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) ITGA2 N95414 0.03 3.3500278 259 227393_at transmembrane protein 16J TMEM16J AW084755 0.01 1.6880668 260 227466_at hypothetical protein LOC285550 LOC285550 BF108695 0.02 1.5282669 261 227771_at leukemia inhibitory factor receptor LIFR AW592684 0.01 2.7902896 262 227808_at DnaJ (Hsp40) homolog, subfamily C, member 15 DNAJC15 AI091398 0.03 1.8649827 263 227998_at S100 calcium binding protein A16 S100A16 AA045184 0.01 2.2575665 264 228152_s_at hypothetical protein FLJ31033 FLJ31033 AK023743 0.02 2.2769616 265 228275_at CDNA FLJ32438 fis, AI200555 0.02 1.813842 clone SKMUS2001402 266 228531_at sterile alpha motif domain containing 9 SAMD9 AA741307 0.02 2.303081 267 228562_at Zinc finger and BTB domain containing 10 ZBTB10 N29918 0.01 2.046323 268 228600_x_at hypothetical protein MGC72075 MGC72075 BE220330 0.02 1.6221175 269 228640_at BH-protocadherin (brain-heart) PCDH7 BE644809 0.03 3.3346767 270 228713_s_at dehydrogenase/reductase (SDR family) member 10 DHRS10 AI742586 0.02 1.9451209 271 228854_at Transcribed locus AI492388 0.03 4.4617124 272 228972_at AI028602 0.02 1.6522069 273 229573_at Transcribed locus AI659456 0.02 1.5438964 274 229582_at chromosome 18 open reading frame 37 C18orf37 AI758919 0.01 1.6219943 275 229997_at vang-like 1 (van gogh, Drosophila) VANGL1 AA789332 0.02 1.6355668 276 230206_at Dedicator of cytokinesis 5 DOCK5 AI692645 0.01 1.7685658 277 230329_s_at nudix (nucleoside diphosphate linked moiety X)-type motif 6 NUDT6 AI580268 0.02 1.5125636 278 230655_at Homo sapiens, clone IMAGE: 5418468, mRNA AW025928 0.01 2.44095 279 230972_at ankyrin repeat domain 9 ANKRD9 AW194999 0.01 1.875526 280 231828_at Homo sapiens, clone IMAGE: 5218355, mRNA AL117474 0.02 2.1623232 281 231832_at UDP-N-acetyl-alpha-D-galactosamine:polypeptide GALNT4 AI890347 0.01 1.8446548 N-acetylgalactosaminyltransferase 4 (GalNAc-T4) 282 234675_x_at CDNA: FLJ23566 fis, clone LNG10880 AK027219 0.01 2.4514613 283 234725_s_at sema domain, immunoglobulin domain (Ig), transmembrane domain SEMA4B AK026133 0.01 1.9406958 (TM) and short cytoplasmic domain, (semaphorin) 4B 284 235015_at Zinc finger, DHHC-type containing 9 ZDHHC9 AL529434 0.01 2.4835925 285 235019_at carboxypeptidase M CPM BE878495 0.02 3.833762 286 235096_at Leo1, Paf1/RNA polymerase II complex component, LEO1 AA074729 0.01 1.5779704 homolog (S. cerevisiae) 287 235648_at zinc finger protein 567 ZNF567 AA742659 0.02 1.6336213 288 235911_at hypothetical gene supported by BC034933; BC068085 LOC440995 AI885815 0.01 4.651685 289 238063_at hypothetical protein FLJ32028 FLJ32028 AA806283 0.01 2.002421 290 238523_at chromosome 16 open reading frame 44 C16orf44 BF941204 0.03 1.5099897 291 238701_x_at FLJ45803 protein FLJ45803 BE176566 0.01 2.3077648 292 238778_at membrane protein, palmitoylated 7 MPP7 AI244661 0.02 3.0538154 (MAGUK p55 subfamily member 7) 293 239896_at Similar to RAB guanine nucleotide exchange factor (GEF) 1 LOC402671 AW190479 0.02 1.6268736 294 241994_at Xanthine dehydrogenase XDH BG260086 0.02 3.2672102 295 241996_at AI669591 0.01 1.7369617 296 244495_x_at chromosome 18 open reading frame 45 C18orf45 AL521157 0.01 1.8056976 297 36553_at acetylserotonin O-methyltransferase-like ASMTL AA669799 0.02 1.6164968 298 36829_at period homolog 1 (Drosophila) PER1 AF022991 0.01 1.9640467 299 55081_at MICAL-like 1 MICAL-L1 W46406 0.02 1.5616423 300 60474_at chromosome 20 open reading frame 42 C20orf42 AA469071 0.01 3.1548133

TABLE 3 Genbank T-test Fold change NO. Probe Set ID Gene Name Gene Symbol Accession # p-value (abs) 001 117_at heat shock 70 kDa protein 6 (HSP70B′) HSPAB X51757 0.03 1.7216957 002 1552486_s_at lactamase, beta LACTB NM_171846 0.02 1.5217854 003 1553530_a_at integrin, beta 1 (fibronectin receptor, ITGB1 NM_033669 0.01 2.0436814 beta polypeptide, antigen CD29 includes MDF2, MSK12) 004 1553694_a_at phosphoinositide-3-kinase, class 2, alpha polypeptide PIK3C2A NM_002645 0.03 1.6315013 005 1553715_s_at hypothetical protein MGC15416 MGC15416 NM_032371 0.02 1.5123988 006 1554747_a_at septin 2 02-Sep BC033559 0.01 1.560747 007 1555326_a_at ADAM metallopeptidase domain 9 (meltrin gamma) ADAM9 AF495383 0.03 2.140922 008 1555060_a_at KIAA1702 protein KIAA1702 AK027074 0.01 1.5686767 009 1557987_at PI-3-kinase-related kinase SMG-1-like locus LOC641298 BC042832 0.01 2.2149343 010 1558678_s_at metastasis associated lung adenocarcinoma transcript MALAT1 BE708432 0.01 2.2265985 1 (non-coding RNA) 011 1560622_at TPA regulated locus TPARL AK000203 0.03 1.5656745 012 1564053_a_at YTH domain family, member 3 YTHDF3 AK093081 0.02 1.8976958 013 1569106_s_at hypothetical protein FLJ10707 FLJ10707 BI087313 0.02 1.5838199 014 200604_s_at protein kinase, cAMP-dependent, regulatory, type I, alpha PRKAR1A M18468 0.02 1.5480618 (tissue specific extinguisher 1) 015 200864_s_at RAB11A, member RAS oncogene family RAB11A NM_004663 0.01 1.5156919 016 200927_s_at RAB14, member RAS oncogene family RAB14 AA919115 0.01 1.607915 017 201152_s_at muscleblind-like (Drosophila) MBNL1 N31913 0.01 1.5028459 018 201194_at selenoprotein W, 1 SEPW1 NM_003009 0.01 1.8139104 019 201362_at influenza virus NS1A binding protein IVNS1ABP AF205218 0.02 1.5876002 020 201363_s_at influenza virus NS1A binding protein IVNS1ABP AB020657 0.01 1.6949687 021 201376_s_at heterogeneous nuclear ribonucleoprotein F HNRPF AI591354 0.01 1.5007194 022 201386_s_at DEAH (Asp-Glu-Ala-His) box polypeptide 15 DHX15 AF279891 0.01 1.7872009 023 201399_s_at translocation associated membrane protein 1 TRAM1 NM_014294 0.01 1.6199075 024 201505_at laminin, beta 1 LAMB1 NM_002291 0.01 2.091507 025 201548_s_at Jumonji, AT rich interactive domain 1B (RBP2-like) JARID1B W02593 0.02 1.5838325 026 201549_x_at Jumonji, AT rich interactive domain 1B (RBP2-like) JARID1B NM_006618 0.02 1.6096623 027 201559_s_at chloride intracellular channel 4 CLIC4 AF109196 0.02 2.2302318 028 201578_at podocalyxin-like PODXL NM_005397 0.01 2.138917 029 201617_x_at caldesmon 1 CALD1 NM_004342 0.02 2.0084002 030 201619_at peroxiredoxin 3 PRDX3 NM_006793 0.01 1.5513384 031 201646_at scavenger receptor class B, member 2 SCARB2 AA885297 0.02 1.6010221 032 201647_s_at scavenger receptor class B, member 2 SCARB2 NM_005506 0.03 1.5906466 033 201661_s_at acyl-CoA synthetase long-chain family member 3 ACSL3 NM_004457 0.01 1.6001148 034 201678_s_at DC12 protein DC12 NM_020187 0.03 1.5643462 035 201787_at fibulin 1 FBLN1 NM_001996 0.03 1.910708 036 201798_s_at fer-1-like 3, myoferlin (C. elegans) FER1L3 NM_013451 0.02 1.6354269 037 201918_at Solute carrier family 25, member 36 SLC25A36 AI927944 0.03 1.6411883 038 201942_s_at carboxypeptidase D CPD D85390 0.02 1.6134206 039 202007_at nidogen 1 NID1 BF940043 0.03 1.784865 040 202143_s_at COP9 constitutive photomorphogenic homolog subunit 8 COPS8 NM_006710 0.02 1.5126611 (Arabidopsis) 041 202374_s_at RAB3 GTPase activating protein subunit 2 (non-catalytic) RAB3GAP2 NM_012414 0.02 1.5766535 042 202429_s_at protein phosphatase 3 (formerly 2B), catalytic subunit, PPP3CA AL353950 0.01 1.7161785 alpha isoform (calcineurin A alpha) 043 202444_s_at SPFH domain family, member 1 SPFH1 NM_006459 0.01 1.8896967 044 202457_s_at protein phosphatase 3 (formerly 2B), catalytic subunit, PPP3CA AA911231 0.01 1.552117 alpha isoform (calcineurin A alpha) 045 202536_at chromatin modifying protein 2B CHMP2B AK002165 0.01 1.5160311 046 202593_s_at membrane interacting protein of RGS16 MIR16 NM_016641 0.02 1.5102472 047 202627_s_at serpin peptidase inhibitor, clade E SERPINE1 AL574210 0.02 3.9358664 (nexin, plasminogen activator inhibitor type 1), member 1 048 202628_s_at serpin peptidase inhibitor, clade E SERPINE1 NM_000602 0.02 3.6850758 (nexin, plasminogen activator inhibitor type 1), member 1 049 202770_s_at cyclin G2 CCNG2 NM_004354 0.03 1.5435082 050 202923_s_at glutamate-cysteine ligase, catalytic subunit GCLC NM_001498 0.02 2.9063768 051 202946_s_at BTB (POZ) domain containing 3 BTBD3 NM_014962 0.01 1.6240557 052 202955_s_at ADP-ribosylation factor guanine nucleotide-exchange factor 1 ARFGEF1 AF084520 0.02 1.5484247 (brefeldin A-inhibited) 053 203066_at B cell RAG associated protein GALNAC4S-6ST NM_014863 0.03 1.5839539 054 203085_s_at transforming growth factor, beta 1 (Camurati-Engelmann disease) TGFB1 BC000125 0.03 2.1608279 055 203293_s_at lectin, mannose-binding, 1 LMAN1 NM_005570 0.02 1.9789635 056 203294_s_at lectin, mannose-binding, 1 LMAN1 U09716 0.02 2.082541 057 203404_at armadillo repeat containing, X-linked 2 ARMCX2 NM_014782 0.02 2.0663633 058 203748_x_at RNA binding motif, single stranded interacting protein 1 RBMS1 NM_016839 0.01 1.6428717 059 204053_x_at phosphatase and tensin homolog (mutated in multiple PTEN U96180 0.02 1.7072555 advanced cancers 1) 060 204066_s_at centaurin, gamma 2 CENTG2 NM_014914 0.03 1.6650882 061 204605_at cell growth regulator with ring finger domain 1 CGRRF1 NM_006568 0.02 1.5059351 062 204790_at SMAD, mothers against DPP homolog 7 (Drosophila) SMAD7 NM_005904 0.03 1.7849346 063 205180_s_at ADAM metallopeptidase domain 8 ADAM8 NM_001109 0.03 1.8976016 064 205436_s_at H2A histone family, member X H2AFX NM_002105 0.01 1.542324 065 205527_s_at gem (nuclear organelle) associated protein 4 GEMIN4 NM_015487 0.03 1.5615736 066 206042_x_at small nuclear ribonucleoprotein polypeptide N SNRPN SNRPN NM_022804 0.02 1.6762362 upstream reading frame 067 206113_s_at RAB5A, member RAS oncogene family RAB5A NM_004162 0.02 1.7590842 068 206116_s_at tropomyosin 1 (alpha) TPM1 NM_000366 0.01 2.168161 069 206245_s_at influenza virus NS1A binding protein IVNS1ABP NM_006469 0.01 1.5090567 070 207266_x_at RNA binding motif, single stranded interacting protein 1 RBMS1 NM_016837 0.01 1.6106415 071 207431_s_at degenerative spermatocyte homolog 1, lipid desaturase (Drosophila) DEGS1 NM_003676 0.01 1.542273 072 207821_s_at PTK2 protein tyrosine kinase 2 PTK2 NM_005607 0.01 1.6032615 073 208097_s_at thioredoxin domain containing TXNDC NM_030755 0.02 1.7288516 074 208643_s_at X-ray repair complementing defective repair in Chinese hamster XRCC5 J04977 0.02 1.5489099 cells 5 (double-strand-break rejoining; Ku autoantigen, 80 kDa) 075 208859_s_at alpha thalassemia/mental retardation syndrome X-linked ATRX AI650257 0.02 1.6250781 (RAD54 homolog, S. cerevisiae) 076 209131_s_at synaptosomal-associated protein, 23 kDa SNAP23 U55936 0.01 1.8967965 077 209209_s_at pleckstrin homology domain containing, family C PLEKHC1 AW469573 0.02 2.2543647 (with FERM domain) member 1 078 209409_at growth factor receptor-bound protein 10 GRB10 D86962 0.02 1.7913702 079 209647_s_at suppressor of cytokine signaling 5 SOCS5 AW664421 0.01 1.5314134 080 209868_s_at RNA binding motif, single stranded interacting protein 1 RBMS1 D28482 0.01 1.757919 081 210154_at malic enzyme 2, NAD(+)-dependent, mitochondrial ME2 M55905 0.03 1.658911 082 210337_s_at ATP citrate lyase ACLY U18197 0.03 1.6132175 083 210809_s_at periostin, osteoblast specific factor POSTN D13665 0.03 1.9660459 084 211202_s_at Jumonji, AT rich interactive domain 1B (RBP2-like) JARID1B AF087481 0.03 1.6053953 085 211559_s_at cyclin G2 CCNG2 L49506 0.03 2.0475583 086 211651_s_at laminin, beta 1 LAMB1 M20206 0.01 2.44758 087 211864_s_at fer-1-like 3, myoferlin (C. elegans) FER1L3 AF207990 0.02 1.9618642 088 211981_at collagen, type IV, alpha 1 COL4A1 NM_001845 0.03 2.0343637 089 211985_s_at calmodulin 1 (phosphorylase kinase, delta) CALM1 AI653730 0.03 1.5034102 090 211992_at WNK lysine deficient protein kinase 1 WNK1 AI445745 0.02 1.5539628 091 212298_at neuropilin 1 NRP1 BE620457 0.02 1.7827071 092 212660_at PHD finger protein 15 PHF15 AI735639 0.02 1.7572457 093 212720_at poly(A) polymerase alpha PAPOLA AI670847 0.02 1.6408824 094 212907_at Solute carrier family 30 (zinc transporter), member 1 SLC30A1 AI972416 0.01 1.739024 095 213012_at neural precursor cell expressed, developmentally down-regulated 4 NEDD4 D42055 0.02 1.6585234 096 213061_s_at N-terminal asparagine amidase NTAN1 AA643304 0.02 1.5069518 097 213901_x_at RNA binding motif protein 9 RBM9 AW149379 0.02 1.5630468 098 214196_s_at tripeptidyl peptidase I TPP1 AA602532 0.02 1.8428509 099 214544_s_at synaptosomal-associated protein, 23 kDa SNAP23 NM_003825 0.02 1.8551272 100 214581_x_at tumor necrosis factor receptor superfamily, member 21 TNFRSF21 BE568134 0.01 1.9035177 101 214701_s_at fibronectin 1 FN1 AJ276395 0.01 2.180369 124 222540_s_at hepatitis B virus x associated protein HBXAP BG286920 0.01 1.678279 125 222693_at fibronectin type III domain containing 3B FNDC3B BF444916 0.02 1.5484349 126 223010_s_at OCIA domain containing 1 OCIAD1 AA454649 0.01 1.638761 127 223110_at KIAA1429 KIAA1429 BC003701 0.02 1.555597 128 223276_at putative small membrane protein NID67 NID67 AF313413 0.02 1.8129323 129 223577_x_at PRO1073 protein PRO1073 AA827878 0.02 2.037919 130 223940_x_at metastasis associated lung adenocarcinoma transcript 1 MALAT1 AF132202 0.01 2.7140348 (non-coding RNA) 131 224567_x_at metastasis associated lung adenocarcinoma transcript 1 MALAT1 BG534952 0.02 2.436764 (non-coding RNA) 132 224726_at mindbomb homolog 1 (Drosophila) MIB1 W80418 0.03 1.5452155 133 224819_at transcription elongation factor A (SII)-like 8 TCEAL8 AI743979 0.01 1.5945034 134 224859_at CD276 antigen CD276 AL360136 0.03 1.5041374 135 225021_at zinc finger protein 532 ZNF532 AA861416 0.02 1.6210703 136 225032_at fibronectin type III domain containing 3B FNDC3B AI141784 0.01 1.5388452 137 225168_at FERM domain containing 4A FRMD4A T78406 0.01 1.8072422 138 225239_at AI355441 0.02 2.2125103 139 225285_at branched chain aminotransferase 1, cytosolic BCAT1 AK025615 0.02 2.027126 140 225424_at glycerol-3-phosphate acyltransferase, mitochondrial GPAM AB046780 0.02 1.740033 141 225567_at Hypothetical LOC388114 LOC388114 BE207755 0.01 1.888815 142 225609_at glutathione reductase GSR AI888037 0.02 2.144665 143 225974_at transmembrane protein 64 TMEM64 BF732480 0.02 1.5707608 144 226280_at BCL2/adenovirus E1B 19 kDa interacting protein 2 BNIP2 AA133277 0.02 1.5715192 145 226558_at Full-length cDNA clone CS0DI062YC15 of Placenta BE856637 0.02 1.6961281 Cot 25-normalized of Homo sapiens (human) 146 226675_s_at metastasis associated, lung adenocarcinoma MALAT1 W80468 0.01 2.2176015 transcript 1 (non-coding RNA) 147 226850_at sulfatase modifying factor 1 SUMF1 AA683501 0.02 1.582926 148 227062_at trophoblast-derived noncoding RNA TncRNA AU155361 0.01 3.1964853 149 227072_at rotatin RTTN BG167480 0.02 1.6342819 150 227080_at zinc finger protein 697 ZNF697 AW003092 0.01 2.047982 151 227257_s_at chromosome 10 open reading frame 46 C10orf46 AW973842 0.02 1.8308182 152 227456_s_at chromosome 6 open reading frame 136 C6orf136 BF224092 0.02 1.5313978 153 229586_at chromodomain helicase DNA binding protein 9 CHD9 AW300405 0.01 1.6146306 154 229606_at Protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform PPP3CA AI827550 0.02 1.5514666 (calcineurin A alpha) 155 229982_at hypothetical protein FLJ21924 FLJ21924 AW195525 0.03 1.5703845 156 231735_s_at PRO1073 protein PRO1073 NM_014086 0.02 2.0209107 157 231823_s_at KIAA1295 KIAA1295 BG054798 0.03 1.527874 158 234989_at trophoblast-derived noncoding RNA TncRNA AV699657 0.02 2.0119648 159 235138_at Pumilio homolog 2 (Drosophila) PUM2 AA565051 0.01 1.7716993 160 235879_at Muscleblind-like (Drosophila) MBNL1 AI697540 0.01 2.2558458 161 236841_at CXYorf1-related protein FLJ25222 BE464132 0.01 1.7994804 162 238549_at core-binding factor, runt domain, alpha subunit 2; translocated to, 2 CBFA2T2 AI420611 0.01 1.928193 163 239742_at Tubby like protein 4 TULP4 H15278 0.03 1.5802637 164 242121_at AW973232 0.03 1.7029374 165 243768_at SUMO1/sentrin specific peptidase 6 SENP6 AA026388 0.01 2.2681193 166 244804_at Sequestosome 1 SQSTM1 AW293441 0.01 1.5338039

In Tables 1, 2 and 3, gene name denotes a name of a gene, gene symbol denotes a symbol representing a gene, and Genbank Accession # denotes a number accessing Gen bank which is a database that the public can access. I-test p value is obtained by statistically analyzing the degree of difference between an average expression level in a patient with lung cancer recurrence and an average expression level in a patient without lung cancer recurrence after lung cancer tissue removal operation.

Here, an expression level was calculated by Affymetrix GeneChip Operating Software (GCOS) Version 1.3 after a hybridization analysis using a microarray on which a probe is immobilized. Fold change (abs) indicates a ratio between an average expression level in a patient with lung cancer recurrence and an average expression level in a patient without lung cancer recurrence after lung cancer tissue removal operation in a hybridization analysis using a microarray on which a probe is immobilized.

As shown in Tables 1, 2 and 3, expression values of at least one marker gene selected from the group consisting of marker genes of Genbank Accession No. shown in Tables 1, 2 and 3 showed statistically meaningful differences such that both T-test p values of the patient with lung cancer recurrence and the patient without lung cancer recurrence were less than 0.05. Therefore, at least one marker gene selected from the group consisting of marker genes of Gen bank Accession No. shown in Tables 1, 2 and 3 can be used as a marker gene that can predict whether lung cancer is recurred afterwards with respect to the patients with a lung cancer removal operation. In addition, at least one marker gene selected from the group consisting of marker genes of Genbank Accession No. shown in Tables 1, 2 and 3 had showed that all the ratios of an expression average of the patients with lung cancer recurrence to an expression average of the patients without lung cancer recurrence was at least 1.5:1. Accordingly, it was confirmed that the expression of the marker gene was significantly increased in the patients with lung cancer recurrence.

DETAILED DESCRIPTION OF THE INVENTION

Hereinafter, the present invention will be described more specifically with reference to the following Examples. The following Examples are for illustrative purposes and are not intended to limit the scope of the invention.

Example Example 1 Selection of Marker Gene Related to Lung Cancer Recurrence

Primary lung cancer tissue having a tumor size of less than 3 cm and without lymph node metastase (that is, N₀M₀T₁ stage) was collected. Total RNA was then immediately isolated from the collected lung cancer tissue. All the collected tumor tissue was lightly dyed with hematoxylin in order to improve visualization prior to RNA extraction. Each finely cut sample comprised at least 90% of tumor cells.

To avoid a necrotic region, one or two pieces of tumor tissue having a size of 5mm×5 mm from the edge of tumor mass was immediately stored at ×80□.

The finely cut tumor tissue was added to 1 ml of a Trizol reagent (Life Technologies, Rockville, Md.), and immediately homogenized by vortexing. Total RNA was isolated according to Trizol reagent protocol. The quality of the isolated total RNA was analyzed by electrophoresis using 1% agarose gel comprising 0.6 M formamide and ethidium bromide. An amount of total RNA was analyzed using a Nanodrop spectrometer (Nanodrop Technologies, Rockland, Del.).

The quality and amount of the isolated total RNA were confirmed to be excellent, and a reverse transcription reaction was performed using the RNA as a template and oligo dT as a primer to obtain cDNA. The obtained cDNA was used as a template that synthesizes cRNA through an in vitro transcription reaction. At this time, cRNA synthesized by adding UTP modified with biotin to a reaction solution was labeled with biotin. Next, the synthesized biotin-labeled cRNA was reacted with a hydroxyl radical to be fragmentized with a size of 50-200 bp. 10 μg of the fragmentized cRNA sample was injected onto an Affymetrix GeneChip array (human 133 plus ver 2) and hybridized at 45□ for 16 hours. The hybridization mixture was then removed and the microarrays were washed, stained with phycoerythrin-labeled Streptavidin, washed, incubated with biotinylated anti-streptavidin, and then restained with phycoerythrin-labeled Streptavidin to amplify the signals. Arrays were scanned using the GeneChip Scanner 3000 7G scanner (Affymetrix), controlled by Affymetrix GeneChip Operating System (GCOS) software. The Affymetrix Microarray Suite version 5 (MAS5) algorithm were utilized to analyze the hybridization intensity data from the microarrays and calculate a set of matrixes that describe probe set performance.

The obtained data was analyzed using an ArrayAssist™ (Stratagene, Inc., San Diego, USA) program. Data preprocessing was performed using a GCRMA (log 2 transformation) method that is a normalization method of multi-microarray level, in which fluorescence intensity values with respect to total microarrays used in analysis were substituted with log 2, and a fluorescence intensity average with respect to the total microarrays was adjusted taking into consideration of a GC amount of a nucleic acid sequence. Comparison between groups was performed under conditions of unpaired t-test, permutation=100, corrected p-value, Number of False Discovery Rate (NO/FDR). Data filtering was performed by selecting only data that satisfied an expression level (recurrence and non-recurrence, group average)>5 and fold change≧1.5. A count for each probeset_id was defined as the number of probe sets that showed a gene expression difference that satisfies the filtering standard in ADC, SQC, or in the recurrence group and non-recurrence group regardless of cell types.

As a result of analysis, the number of markers selected as positive expression with respect to adenocarcinoma (ADC) and squamous cell carcinoma (SQC) are shown in Table 4 below.

TABLE 4 total lung squamous cell cancer tissue adenocarcinoma carcinoma number of probe 166 300 166

Data related to expression of each gene that was obtained by the measurement of fluorescence intensity was obtained. To confirm correlation between the collected data related to expression of gene and lung cancer recurrence, patients with a lung cancer removal operation were monitored for five years to confirm lung cancer recurrence or non-recurrence. In the case of patients with lung cancer recurrence within one year after a lung cancer removal operation, they were grouped into a lung cancer recurrence group. In the case of patients without lung cancer recurrence even after three years after a lung cancer removal operation, they were grouped into a non-recurrence group. Data with respect to the obtained recurrence group and non-recurrence group among patients with a lung cancer removal operation was obtained.

Next, correlation between an expression pattern of each gene which was analyzed during the lung cancer removal operation, and the recurrence and non-recurrence groups that were subsequently obtained by monitoring the patients with a lung cancer removal operation was analyzed. The results are shown in Tables 1, 2 and 3.

Table 1 represents the results in which the gene expression pattern of the lung cancer cell after lung cancer tissue removal operation is analyzed through hybridization with a probe on a microarray, and a marker gene is selected, the marker gene being determined to have a difference in an expression level between a patient with lung cancer recurrence within one year and a patient without lung cancer recurrence even after three years. The total number of patients was 60. Among them, the number of patients with lung cancer recurrence within one year after lung cancer tissue removal operation was 19, and the number of patients without lung cancer recurrent even after three years was 41.

Table 2 represents the results in which the gene expression pattern of the lung cancer cell which was classified into adenocarcinoma after lung cancer tissue removal operation is analyzed through hybridization with a probe on a microarray, and a marker gene is selected, the marker gene being determined to have a difference in an expression level between a patient with lung cancer recurrence within one year and a patient without lung cancer recurrence even after three years. A total number of adenocarcinoma patients was 23. Among them, the number of patients with lung cancer recurrence within one year after lung cancer tissue removal operation was 8, and the number of patients without lung cancer recurrent even after three years was 15.

Table 3 represents the results in which the gene expression pattern of the lung cancer cell which was classified into squamous cell carcinoma after lung cancer tissue removal operation is analyzed through hybridization with a probe on a microarray, and a marker gene is selected, the marker gene being determined to have a difference in an expression level between a patient with lung cancer recurrence within one year and a patient without lung cancer recurrence even after three years. The total number of squamous cell carcinoma patients was 37. Among them, the number of patients with lung cancer recurrence within one year after lung cancer tissue removal operation was 11, and the number of patients without lung cancer recurrent even after three years was 26.

As shown in Tables 1, 2 and 3, expression values of at least one marker gene selected from the group consisting of marker genes of Genbank Accession No. shown in Tables 1, 2 and 3 showed statistically meaningful differences such that both T-test p values of the patient with lung cancer recurrence and the patient without lung cancer recurrence were less than 0.05. Therefore, at least one marker gene selected from the group consisting of marker genes of Genbank Accession No. shown in Tables 1, 2 and 3 can be used as a marker gene that can predict whether lung cancer is likely to recur with respect to the patients that have had a lung cancer removal operation. In addition, at least one marker gene selected from the group consisting of marker genes of Genbank Accession No. shown in Tables 1, 2 and 3 showed that all the ratios of an expression average of the patients with lung cancer recurrence to an expression average of the patients without lung cancer recurrence were at least 1.5:1. Accordingly, it was confirmed that the expression of the marker gene was significantly increased in the patients with lung cancer recurrence.

The relationships between lung cancer recurrence in patients after lung cancer removal operation and conditions of the patients such as age, sex, smoking, cell type, pstage, and tumor size were analyzed, and the results are shown in Tables 5, 6 and 7.

TABLE 5 variation statistical analysis method result sex chi-square test no difference: p value = 0.552 age 2-sample t-test no difference: p value = 0.559 smoking chi-square test no difference: p value = 0.813 cell type chi-square test no difference: p value = 0.682 pstage Fisher's exact test no difference: p value = 0.305 tumor size 2-sample t-test difference: p value = 0.039 metastasis — no metastasis

Table 5 shows results of analyzing 60 patients without classifying them according to cell types of lung cancer. Among 60 patients, the number of patients with lung cancer recurrence was 19, and the number of patients without lung cancer recurrence was 41. As shown in Table 5, the clinical indexes from the all patients looked no statistically meaningful difference in the recurrence group and the non-recurrence group. That is, the analyzed result can be regarded as a gene list that represents statistically meaningful difference in expression only with respect to the recurrence.

TABLE 6 variation statistical analysis method result sex Fisher's exact test no difference: p value = 1.000 age 2-sample t-test no difference: p value = 0.618 smoking chi-square test no difference: p value = 0.6570 cell type — adenocarcinoma (ADC) pstage Fisher's exact test no difference: p value = 0.085 tumor size 2-sample t-test no difference: p value = 0.051 metastasis — no metastasis

Table 6 shows results of analyzing 23 patients having adenocarcinoma when they are classified according to cell types of lung cancer. Among 23 patients, the number of patients with lung cancer recurrence was 8, and the number of patients without lung cancer recurrence was 15. As shown in Table 6, clinical information except the recurrence and tumor size which may induce confounding in other analysis may not have any statistically meaningful difference in the recurrence group and the non-recurrence group. That is, the analyzed result can be regarded as a gene list that represents statistically meaningful difference in expression only with respect to the recurrence.

TABLE 7 variation statistical analysis method result sex — man age 2-sample t-test no difference: p value = 0.328 smoking chi-square test no difference: p value = 1.000 cell type — squamous cell carcinoma (SQC) pstage Fisher's exact test no difference: p value = 1.000 tumor size 2-sample t-test no difference: p value = 0.417 metastasis — no metastasis

Table 7 shows results of analyzing 37 patients having squamous cell carcinoma when they are classified according to cell types of lung cancer. Among 23 patients, the number of patients with lung cancer recurrence was 11, and the number of patients without lung cancer recurrence was 26. As shown in Table 7, clinical information except the recurrence and tumor size which may induce confounding in other analysis may not have any statistically meaningful difference in the recurrence group and the non-recurrence group. That is, the analyzed result can be regarded as a gene list that represents statistically meaningful difference in expression only with respect to the recurrence.

Example 2 Prediction of Risk of Lung Cancer Recurrence Using Statistical Model

Based on the expression level of marker genes collected from the patients with lung cancer recurrence and non-recurrence which were obtained in Example 1, it was confirmed whether a risk of lung cancer recurrence could be predicted using a statistical analysis model.

In the analysis, a portion of each of data obtained with respect to total lung cancer tissue, adenocarcinoma and squamous cell carcinoma was used as a learning set to establish a basis on the prediction accuracy of the statistical model, the other portion of the data was used to identify whether the establish prediction accuracy is actually accurate using the leaning set

Data of learning sets and test sets with respect to the total lung cancer tissue, adenocarcinoma and squamous cell carcinoma are shown in Tables 8, 9 and 10.

TABLE 8 total lung cancer tissue non-recurrence recurrence total learning set 28 15 43 test set 13 4 17 total 41 19 60

TABLE 9 adenocarcinoma non-recurrence recurrence total learning set 9 6 15 test set 6 2 8 total 16 8 23

TABLE 10 squamous cell carcinoma non-recurrence recurrence total learning set 17 7 24 test set 9 4 13 total 26 11 37

Results of predicting the test set with respect to the lung cancer tissue, adenocarcinoma and squamous cell carcinoma using a QDA prediction model are shown in Tables 11, 12 and 13 below. As shown in Tables 11, 12 and 13, the overall accuracy was at least 76.4%.

TABLE 11 Predicted results of the total lung cancer tissue using a QDA prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 10 1 11 recurrence 3 3 6 overall accuracy 76.4%

The overall accuracy in Table 11 is a percentage of predicted class which corresponds to true class per total sample. That is, the overall accuracy is (17-4)×100/17=76.4%. The total is calculated in the same manner described above.

TABLE 12 Predicted results of adenocarcinoma tissue using a QDA prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 6 0 6 recurrence 0 2 2 overall accuracy 100%

TABLE 13 Predicted results of squamous cell carcinoma tissue using a QDA prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 9 2 11 recurrence 0 2 2 overall accuracy 84.6%

Results of predicting the test set with respect to the lung cancer tissue, adenocarcinoma and squamous cell carcinoma using a Linear Discrimination Analysis (LDA) prediction model are shown in Tables 14, 15 and 16 below. As shown in Tables 14, 15 and 16, the overall accuracy was at least 76.4%.

TABLE 14 Predicted results of the total lung cancer tissue using a LDA prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 10 1 11 recurrence 3 3 6 overall accuracy 76.4%

TABLE 15 Predicted results of adenocarcinoma tissue using a LDA prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 6 0 6 recurrence 0 2 2 overall accuracy 100%

TABLE 16 Predicted results of squamous cell carcinoma tissue usinq a LDA prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 9 1 10 recurrence 0 3 3 overall accuracy 92.3%

Results of predicting the test set with respect to the lung cancer tissue, adenocarcinoma and squamous cell carcinoma using a Neural network prediction model are shown in Tables 17, 18 and 19 below. As shown in Tables 17, 18 and 19, the overall accuracy was at least 59.46%.

TABLE 17 Predicted results of the total lung cancer tissue using a Neural network prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 40 1 41 recurrence 18 1 19 overall accuracy 68.33%

TABLE 18 Predicted results of adenocarcinoma tissue using a Neural network prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 14 1 15 recurrence 1 7 8 overall accuracy 91.3%

TABLE 19 Predicted results of squamous cell carcinoma tissue using a Neural network prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 20 6 26 recurrence 9 2 11 overall accuracy 59.46%

Results of predicting the test set with respect to the lung cancer tissue, adenocarcinoma and squamous cell carcinoma using a Decision tree prediction model are shown in Tables 20, 21 and 22 below. As shown in Tables 20, 21 and 22, the overall accuracy was at least 61.67%.

TABLE 20 Predicted results of the total lung cancer tissue using a Decision tree prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 35 6 41 recurrence 17 2 19 overall accuracy 61.67%

TABLE 21 Predicted results of adenocarcinoma tissue using a Decision tree prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 15 0 15 recurrence 8 0 8 overall accuracy 65.22%

TABLE 22 Predicted results of squamous cell carcinoma tissue using a Decision tree prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 25 1 26 recurrence 2 9 11 overall accuracy 91.89%

Results of predicting the test set with respect to the lung cancer tissue, adenocarcinoma and squamous cell carcinoma using a Support vector machine prediction model are shown in Tables 23, 24 and 25 below. As shown in Tables 23, 24 and 25, the overall accuracy was at least 65%.

TABLE 23 Predicted results of the total lung cancer tissue using a Support vector machine prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 37 4 41 recurrence 17 2 19 overall accuracy 65%

TABLE 24 Predicted results of adenocarcinoma tissue using a Support vector machine prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 15 0 15 recurrence 1 7 8 overall accuracy 95.65%

TABLE 25 Predicted results of squamous cell carcinoma tissue using a Support vector machine prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 24 2 26 recurrence 1 10 11 overall accuracy 91.89%

Results of predicting the test set with respect to the lung cancer tissue, adenocarcinoma and squamous cell carcinoma using a Naive Bayes prediction model are shown in Tables 26, 27 and 28 below. As shown in Tables 26, 27 and 28, the overall accuracy was at least 58.33%.

TABLE 26 Predicted results of the total lung cancer tissue using a Naive Bayes prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 26 15 41 recurrence 10 9 19 overall accuracy 58.33%

TABLE 27 Predicted results of adenocarcinoma tissue using a Naive Bayes prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 15 0 15 recurrence 1 7 8 overall accuracy 95.65%

TABLE 28 Predicted results of squamous cell carcinoma tissue using a Naive Bayes prediction model predicted class classification non-recurrence recurrence total true class non-recurrence 24 2 26 recurrence 1 10 11 overall accuracy 91.89%

The prediction models utilized in Examples of the present invention could have been easily understood by one of ordinary skill in the art (SAS Language: Reference, Version 6, First Edition by the SAS Institute.).

According to the method of predicting risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment according to the present invention, the risk of lung cancer recurrence in a lung cancer patient after a lung cancer removal operation can be predicted with high accuracy.

According to the method of preparing a report on the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment according to the present invention, the report can be prepared to include results predicting the risk of lung cancer recurrence in a lung cancer patient after a lung cancer removal operation with high accuracy.

The report on the risk of lung cancer recurrence in a lung cancer patient or after the patient has lung cancer treatment according to the present invention includes highly accurate results predicting the risk of lung cancer recurrence in a lung cancer patient after a lung cancer removal operation.

According to the composition, kit and microarray for diagnosing the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment according to the present invention, diagnosis efficiency of risk of lung cancer recurrence of a lung cancer patient after a lung cancer treatment can be increased.

While the present invention has been particularly shown and described with reference to exemplary embodiments thereof, it will be understood by those of ordinary skill in the art that various changes in form and details may be made therein without departing from the spirit and scope of the present invention as defined by the following claims. 

1. A method of predicting risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, the method comprising: obtaining a biological sample from a lung cancer patient; measuring an expression level of at least one marker gene from the biological sample, the marker gene being selected from the group consisting of marker genes of Table 1, 2 or 3, to obtain data for the expression level of the marker gene; and determining whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group.
 2. The method of claim 1, wherein the obtaining of a biological sample is performed by obtaining lung cancer tissue.
 3. The method of claim 1, wherein the measuring of an expression level of a marker gene is performed by measuring an expression level of at least one marker gene selected from the group consisting of marker genes of Table
 1. 4. The method of claim 1, wherein the lung cancer is adenocarcinoma and the measuring of an expression level of a marker gene is performed by measuring an expression level of at least one marker gene selected from the group consisting of marker genes of Table
 2. 5. The method of claim 1, wherein the lung cancer is a squamous cell carcinoma and the measuring of an expression level of a marker gene is performed by measuring an expression level of at least one marker gene selected from the group consisting of marker genes of Table
 3. 6. The method of claim 1, wherein the measuring of an expression level of a marker gene is performed by measuring a level of mRNA or protein derived from the maker gene.
 7. The method of claim 1, wherein the determining of whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group is performed using a statistical forecasting model.
 8. The method of claim 7, wherein the statistical forecasting model is selected from the group consisting of an Linear Discrimination Analysis (LDA) model, Quadratic Discriminantion Analysis (QDA) prediction model, a Neural Network model, a Decision Tree model, a Support Vector Machine model and a Naive Bayes model.
 9. The method of claim 1, wherein the determining of whether the expression level of the marker gene corresponds to an expression level of a recurrence group or an expression level of a non-recurrence group comprises determining the marker gene to correspond to a non-recurrence group if the expression level of the marker gene shows a statistically meaningful difference from the expression level of the recurrence group, or determining the marker gene to correspond to a recurrence group if the expression level of the marker gene shows a statistically meaningful difference from the expression level of the non-recurrence group.
 10. The method of claim 9, wherein the statistically meaningful difference is expressed as a p value that indicates a statistical meaning regarding the expression level of the recurrence group or the non-recurrence group.
 11. The method of claim 10, wherein the p value is less than 0.05.
 12. The method of claim 1, wherein the expression level is measured on a microarray.
 13. The method of claim 12, wherein the microarray is a nucleic acid microarray.
 14. The method of claim 1, wherein the expression level of the marker gene is determined by measuring the amount of an amplification product obtained by nucleic acid amplification that is carried out by a reverse transcriptase-polymerase chain reaction (RT-PCR) using RNA isolated from the biological sample as a template.
 15. The method of claim 1, wherein the expression level is measured by detecting protein coded by the marker gene.
 16. The method of claim 15, wherein the detecting of protein is performed by using an antibody specific to the protein.
 17. A method of preparing a report on the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, the method comprising preparing a report representing predicted results according to claim
 1. 18. The method of claim 17, wherein the report comprises probability of recurrence according to time.
 19. A report on a risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, which is prepared by the method according to claim
 17. 20. A composition for diagnosing the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, comprising at least one probe or probe set selected from marker genes selected from the group consisting of marker genes of Tables 1, 2 and
 3. 21. A kit for diagnosing the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, the kit comprising at least one probe or probe set selected from marker genes selected from the group consisting of marker genes of Tables 1, 2 and
 3. 22. The kit of claim 21, wherein the probe or probe set is immobilized on a microarray.
 23. A kit for diagnosing the risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, comprising a sense and anti-sense primer pair for each of at least one marker gene selected from the group consisting of marker genes of Tables 1, 2 and
 3. 24. A microarray for diagnosing a risk of lung cancer recurrence in a lung cancer patient or after a patient has lung cancer treatment, in which at least one probe or probe set selected from marker genes selected from the group consisting of marker genes of Tables 1, 2 and 3 is immobilized on a substrate. 